From eb79a2f1cabf08f2631abcf2a0f75fd3c6fcdfd9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:28:17 +0200 Subject: [PATCH 1/2] update modules --- modules.json | 30 +++++----- modules/nf-core/cnvkit/batch/environment.yml | 5 +- modules/nf-core/cnvkit/batch/main.nf | 11 +++- modules/nf-core/cnvkit/batch/meta.yml | 8 ++- .../gatk4/annotateintervals/environment.yml | 2 +- .../nf-core/gatk4/annotateintervals/main.nf | 4 +- .../annotateintervals/tests/main.nf.test.snap | 58 +++++++++++++------ .../gatk4/bedtointervallist/environment.yml | 2 +- .../nf-core/gatk4/bedtointervallist/main.nf | 4 +- .../gatk4/collectreadcounts/environment.yml | 2 +- .../nf-core/gatk4/collectreadcounts/main.nf | 4 +- .../environment.yml | 2 +- .../createreadcountpanelofnormals/main.nf | 4 +- .../environment.yml | 5 -- .../determinegermlinecontigploidy/main.nf | 4 +- .../gatk4/filterintervals/environment.yml | 2 +- modules/nf-core/gatk4/filterintervals/main.nf | 4 +- .../gatk4/germlinecnvcaller/environment.yml | 5 -- .../nf-core/gatk4/germlinecnvcaller/main.nf | 6 +- .../gatk4/intervallisttools/environment.yml | 2 +- .../nf-core/gatk4/intervallisttools/main.nf | 4 +- .../gatk4/preprocessintervals/environment.yml | 2 +- .../nf-core/gatk4/preprocessintervals/main.nf | 4 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 18 +++--- .../nf-core/samtools/faidx/environment.yml | 5 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 4 ++ .../nf-core/samtools/index/environment.yml | 3 +- modules/nf-core/samtools/index/main.nf | 4 +- .../nf-core/samtools/index/tests/main.nf.test | 36 ++++++------ .../samtools/index/tests/main.nf.test.snap | 54 +++++++++++++++-- 33 files changed, 196 insertions(+), 112 deletions(-) delete mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml delete mode 100644 modules/nf-core/gatk4/germlinecnvcaller/environment.yml diff --git a/modules.json b/modules.json index 2d4ca0a..e6a9a92 100644 --- a/modules.json +++ b/modules.json @@ -7,27 +7,27 @@ "nf-core": { "cnvkit/batch": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f53b071421340e6fac0806c86ba030e578e94826", "installed_by": ["modules"] }, "gatk4/annotateintervals": { "branch": "master", - "git_sha": "42ae163c3c6eb23646189c30c07a889ad39c9b0e", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d3f215802f696f7993f25c759781d2db91232015", "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "gatk4/createreadcountpanelofnormals": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "gatk4/createsomaticpanelofnormals": { @@ -37,12 +37,12 @@ }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "60a7dbae179bcfa24c10294cc9a07423a239c19a", "installed_by": ["modules"] }, "gatk4/filterintervals": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { @@ -52,32 +52,32 @@ }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "cf607b7749da0a8f5ca2a1e31233e13e3159e2fe", "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "5fd04feb37b58caa6a54d41e38c80066bdf71056", "installed_by": ["bam_create_som_pon_gatk"] }, "gatk4/preprocessintervals": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0", "installed_by": ["modules"] }, "picard/createsequencedictionary": { @@ -87,12 +87,12 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] } } diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml index a73ba50..10c5d6b 100644 --- a/modules/nf-core/cnvkit/batch/environment.yml +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -1,8 +1,11 @@ name: cnvkit_batch + channels: - conda-forge - bioconda - defaults + dependencies: - bioconda::cnvkit=0.9.10 - - bioconda::samtools=1.18 + - bioconda::htslib=1.19.1 + - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 33a1dfa..9e8aafa 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -4,8 +4,8 @@ process CNVKIT_BATCH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:f0ad4c1f9b5c0749c12c7a93277ad6f4319b6b72-0' : - 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:f0ad4c1f9b5c0749c12c7a93277ad6f4319b6b72-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' : + 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }" input: tuple val(meta), path(tumor), path(normal) @@ -32,6 +32,7 @@ process CNVKIT_BATCH { def tumor_exists = tumor ? true : false def normal_exists = normal ? true : false + def reference_exists = reference ? true : false // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false @@ -62,6 +63,10 @@ process CNVKIT_BATCH { else { normal_args = normal_prefix ? "--normal $normal_out" : "" } + if (reference_exists){ + fasta_args = "" + normal_args = "" + } } // generation of panel of normals @@ -73,7 +78,7 @@ process CNVKIT_BATCH { tumor_out = "" } - def target_args = targets ? "--targets $targets" : "" + def target_args = targets && !reference_exists ? "--targets $targets" : "" def reference_args = reference ? "--reference $reference" : "" def samtools_cram_convert = '' diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index 4f88ba3..f14efe5 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -18,7 +18,7 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - tumour: + - tumor: type: file description: | Input tumour sample bam file (or cram) @@ -49,7 +49,7 @@ input: description: | Groovy Map containing information about target file e.g. [ id:'test' ] - - targetfile: + - targets: type: file description: | Input target bed file @@ -62,6 +62,10 @@ input: type: file description: | Input reference cnn-file (only for germline and tumor-only running) + - panel_of_normals: + type: file + description: | + Input panel of normals file output: - meta: type: map diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 6e91596..523753c 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index da7acd0..dfe9dc2 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap index 16f81c3..749f6fb 100644 --- a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ], "annotated_intervals": [ [ @@ -24,11 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] } ], - "timestamp": "2023-12-31T01:23:13.232383464" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:07:36.32193" }, "homo_sapiens genome [interval_list]": { "content": [ @@ -43,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ], "annotated_intervals": [ [ @@ -55,11 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] } ], - "timestamp": "2023-12-31T01:23:44.26211215" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:08:12.533176" }, "homo_sapiens genome multi-interval [bed]": { "content": [ @@ -74,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ], "annotated_intervals": [ [ @@ -86,11 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] } ], - "timestamp": "2023-12-31T01:23:28.481436232" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:07:54.643276" }, "homo_sapiens genome [interval_list] mappable_regions": { "content": [ @@ -105,7 +117,7 @@ ] ], "1": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ], "annotated_intervals": [ [ @@ -117,20 +129,28 @@ ] ], "versions": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] } ], - "timestamp": "2023-12-31T01:24:00.492783484" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:08:31.311782" }, "homo_sapiens genome [bed] - stub": { "content": [ [ "test.tsv", - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] ], - "timestamp": "2023-12-31T01:24:29.485750561" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:09:04.54745" }, "homo_sapiens genome [interval_list] duplication_regions": { "content": [ @@ -145,7 +165,7 @@ ] ], "1": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ], "annotated_intervals": [ [ @@ -157,10 +177,14 @@ ] ], "versions": [ - "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + "versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0" ] } ], - "timestamp": "2023-12-31T01:24:15.933897396" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:08:49.684766" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index e7cb428..d6fbe2e 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 88b24b1..68863d6 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index ebc8380..d09cd89 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 1cc3694..2c545d2 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -4,8 +4,8 @@ process GATK4_COLLECTREADCOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index ea5b9bf..b4f4e77 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf index 9d32a99..332f9d9 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATEREADCOUNTPANELOFNORMALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(counts) diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml deleted file mode 100644 index c30de09..0000000 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: gatk4_determinegermlinecontigploidy -channels: - - conda-forge - - bioconda - - defaults diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 5af101f..71a67f7 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -4,7 +4,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { label 'process_single' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package + container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package input: tuple val(meta), path(counts), path(bed), path(exclude_beds) @@ -39,6 +39,8 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { avail_mem = (task.memory.mega*0.8).intValue() } """ + export THEANO_FLAGS="base_compiledir=\$PWD" + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ DetermineGermlineContigPloidy \\ ${input_list} \\ diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index a1d59f2..853995e 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index a6d4702..bf1f3a0 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_FILTERINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml deleted file mode 100644 index 02ce4dd..0000000 --- a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: gatk4_germlinecnvcaller -channels: - - conda-forge - - bioconda - - defaults diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index f42ceb6..cd1916e 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -3,7 +3,7 @@ process GATK4_GERMLINECNVCALLER { label 'process_single' //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package + container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) @@ -37,7 +37,9 @@ process GATK4_GERMLINECNVCALLER { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g -XX:-UsePerfData" \\ + export THEANO_FLAGS="base_compiledir=\$PWD" + + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ GermlineCNVCaller \\ $input_list \\ $ploidy_command \\ diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index b70e5e1..a4026f9 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 10baa75..400fa03 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOOLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index 542d9ef..ec0b09e 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index 61b281d..dffc4bb 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -4,8 +4,8 @@ process GATK4_PREPROCESSINTERVALS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb6..72e598b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.22.2 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352..e59efef 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.22.2--pyhdfd78af_0' : + 'biocontainers/multiqc:1.22.2--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd80..a170c31 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-06-10T11:50:10.874341679" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-06-10T11:50:49.271943761" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,ddbc971a8307f9b9b7b973714cde29d0" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-06-10T11:50:34.046706025" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 01ccbcc..f8450fa 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,7 +1,10 @@ name: samtools_faidx + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.18 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index d346162..bdcdbc9 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index e189af2..f3c25de 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -39,6 +39,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - fa: + type: file + description: FASTA file + pattern: "*.{fa}" - fai: type: file description: FASTA index file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 296ed99..260d516 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8ad18fd..b523c21 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index c76a916..bb7756d 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/index" - test("sarscov2 [BAI]") { + test("bai") { when { params { @@ -16,10 +16,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -28,12 +28,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.bai).match("bai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("bai_versions") } ) } } - test("homo_sapiens [CRAI]") { + test("crai") { when { params { @@ -41,10 +41,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) """ } } @@ -53,12 +53,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.crai).match("crai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("crai_versions") } ) } } - test("homo_sapiens [CSI]") { + test("csi") { config "./csi.nextflow.config" @@ -68,10 +68,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -80,7 +80,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("csi_versions") } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index b3baee7..52756e8 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,28 +1,74 @@ { + "crai_versions": { + "content": [ + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:04.203740976" + }, + "csi_versions": { + "content": [ + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:09.57475878" + }, "crai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" ] ] ], - "timestamp": "2023-11-15T15:17:37.30801" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:41:38.446424" }, "bai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" ] ] ], - "timestamp": "2023-11-15T15:17:30.869234" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:40:46.579747" + }, + "bai_versions": { + "content": [ + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:41:57.929287369" } } \ No newline at end of file From 6b48b1310cd312b9e50d9433dfc3f3542c9e5f7c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 11 Jun 2024 16:54:59 +0200 Subject: [PATCH 2/2] more updates --- .../cnvkit/batch/tests/batch_hybrid.config | 6 + .../cnvkit/batch/tests/batch_pon.config | 6 + .../batch/tests/batch_tumouronly.config | 6 + .../cnvkit/batch/tests/batch_wgs.config | 6 + .../nf-core/cnvkit/batch/tests/main.nf.test | 284 ++++++++++++++ .../cnvkit/batch/tests/main.nf.test.snap | 86 +++++ modules/nf-core/cnvkit/batch/tests/tags.yml | 2 + .../bedtointervallist/tests/main.nf.test | 38 ++ .../bedtointervallist/tests/main.nf.test.snap | 35 ++ .../gatk4/bedtointervallist/tests/tags.yml | 2 + .../determinegermlinecontigploidy/README.md | 9 + .../nf-core/gatk4/germlinecnvcaller/README.md | 9 + .../gatk4/indexfeaturefile/tests/main.nf.test | 105 +++++ .../indexfeaturefile/tests/main.nf.test.snap | 132 +++++++ .../gatk4/indexfeaturefile/tests/tags.yml | 2 + .../intervallisttools/tests/main.nf.test | 72 ++++ .../intervallisttools/tests/main.nf.test.snap | 88 +++++ .../intervallisttools/tests/nextflow.config | 5 + .../gatk4/intervallisttools/tests/tags.yml | 2 + .../nf-core/gatk4/mutect2/tests/f1r2.config | 3 + .../nf-core/gatk4/mutect2/tests/main.nf.test | 360 ++++++++++++++++++ .../gatk4/mutect2/tests/main.nf.test.snap | 204 ++++++++++ .../nf-core/gatk4/mutect2/tests/mito.config | 3 + .../nf-core/gatk4/mutect2/tests/pair.config | 3 + modules/nf-core/gatk4/mutect2/tests/tags.yml | 2 + .../nf-core/samtools/faidx/tests/main.nf.test | 122 ++++++ .../samtools/faidx/tests/main.nf.test.snap | 249 ++++++++++++ .../samtools/faidx/tests/nextflow.config | 7 + .../samtools/faidx/tests/nextflow2.config | 6 + modules/nf-core/samtools/faidx/tests/tags.yml | 2 + tests/pipeline/cnvkit.nf.test.snap | 20 +- tests/test_assets/gens_software_versions.yaml | 10 +- .../germlinecnvcaller_software_versions.yaml | 18 +- 33 files changed, 1884 insertions(+), 20 deletions(-) create mode 100644 modules/nf-core/cnvkit/batch/tests/batch_hybrid.config create mode 100644 modules/nf-core/cnvkit/batch/tests/batch_pon.config create mode 100644 modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config create mode 100644 modules/nf-core/cnvkit/batch/tests/batch_wgs.config create mode 100644 modules/nf-core/cnvkit/batch/tests/main.nf.test create mode 100644 modules/nf-core/cnvkit/batch/tests/main.nf.test.snap create mode 100644 modules/nf-core/cnvkit/batch/tests/tags.yml create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/tags.yml create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/README.md create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/README.md create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/nextflow.config create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/tags.yml create mode 100644 modules/nf-core/gatk4/mutect2/tests/f1r2.config create mode 100644 modules/nf-core/gatk4/mutect2/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/mutect2/tests/mito.config create mode 100644 modules/nf-core/gatk4/mutect2/tests/pair.config create mode 100644 modules/nf-core/gatk4/mutect2/tests/tags.yml create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config create mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml diff --git a/modules/nf-core/cnvkit/batch/tests/batch_hybrid.config b/modules/nf-core/cnvkit/batch/tests/batch_hybrid.config new file mode 100644 index 0000000..07a21b1 --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/batch_hybrid.config @@ -0,0 +1,6 @@ +process { + + withName: CNVKIT_BATCH { + ext.args = '--output-reference reference.cnn' + } +} diff --git a/modules/nf-core/cnvkit/batch/tests/batch_pon.config b/modules/nf-core/cnvkit/batch/tests/batch_pon.config new file mode 100644 index 0000000..3897370 --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/batch_pon.config @@ -0,0 +1,6 @@ +process { + + withName: CNVKIT_BATCH { + ext.args = '--method wgs --output-reference panel_of_normals.cnn' + } +} diff --git a/modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config b/modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config new file mode 100644 index 0000000..91074ff --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config @@ -0,0 +1,6 @@ +process { + + withName: CNVKIT_BATCH { + ext.args = '--method wgs' + } +} diff --git a/modules/nf-core/cnvkit/batch/tests/batch_wgs.config b/modules/nf-core/cnvkit/batch/tests/batch_wgs.config new file mode 100644 index 0000000..48fc879 --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/batch_wgs.config @@ -0,0 +1,6 @@ +process { + + withName: CNVKIT_BATCH { + ext.args = '--output-reference reference.cnn --method wgs' + } +} diff --git a/modules/nf-core/cnvkit/batch/tests/main.nf.test b/modules/nf-core/cnvkit/batch/tests/main.nf.test new file mode 100644 index 0000000..b2c0a9b --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/main.nf.test @@ -0,0 +1,284 @@ +nextflow_process { + + name "Test Process CNVKIT_BATCH" + script "../main.nf" + process "CNVKIT_BATCH" + + tag "modules" + tag "modules_nfcore" + tag "cnvkit" + tag "cnvkit/batch" + + test("cnvkit batch hybrid mode - bam") { + + config "./batch_hybrid.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + println process.out.bed[0][1] + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + test("cnvkit batch wgs - bam") { + + config "./batch_wgs.config" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + test("cnvkit batch wgs - cram") { + + config "./batch_wgs.config" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + test("cnvkit batch tumouronly mode - bam") { + + config "./batch_tumouronly.config" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + [] + ] + input[1] = [[:],[]] + input[2] = [[:],[]] + input[3] = [[:],[]] + input[4] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + test("cnvkit batch tumouronly mode - cram") { + + config "./batch_tumouronly.config" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + [] + ] + input[1] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],[]] + input[4] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + test("cnvkit batch germline mode - cram") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + [], + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)] + input[2] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)] + input[3] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + + test("cnvkit batch germline hybrid mode - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + + test("cnvkit batch pon mode - bam") { + + config "./batch_pon.config" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + [], + [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + ] + ] + input[1] = [[:],file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.version).match() } + ) + } + + } + + + test("cnvkit batch - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) + ] + input[1] = [[:],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[:],[]] + input[3] = [[:],file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)] + input[4] = [[:],[]] + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bed).match() } + ) + } + + } + +} diff --git a/modules/nf-core/cnvkit/batch/tests/main.nf.test.snap b/modules/nf-core/cnvkit/batch/tests/main.nf.test.snap new file mode 100644 index 0000000..5d7cb14 --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/main.nf.test.snap @@ -0,0 +1,86 @@ +{ + "cnvkit batch tumouronly mode - bam": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:30:55.150317561" + }, + "cnvkit batch tumouronly mode - cram": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:31:31.039652656" + }, + "cnvkit batch - bam - stub": { + "content": [ + [ + [ + { + "id": "test" + }, + [ + "baits.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e", + "baits.target.bed:md5,26d25ff2d6c45b6d92169b3559c6acdb" + ] + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:33:25.790391941" + }, + "cnvkit batch wgs - bam": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:30:10.677690173" + }, + "cnvkit batch germline hybrid mode - bam": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:32:50.217076532" + }, + "cnvkit batch hybrid mode - bam": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T13:54:41.69602289" + }, + "cnvkit batch wgs - cram": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:30:27.271060826" + }, + "cnvkit batch pon mode - bam": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:33:06.391306794" + }, + "cnvkit batch germline mode - cram": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T14:32:23.38326412" + } +} \ No newline at end of file diff --git a/modules/nf-core/cnvkit/batch/tests/tags.yml b/modules/nf-core/cnvkit/batch/tests/tags.yml new file mode 100644 index 0000000..1c8565c --- /dev/null +++ b/modules/nf-core/cnvkit/batch/tests/tags.yml @@ -0,0 +1,2 @@ +cnvkit/batch: + - "modules/nf-core/cnvkit/batch/**" diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test new file mode 100644 index 0000000..2289f73 --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process GATK4_BEDTOINTERVALLIST" + script "../main.nf" + process "GATK4_BEDTOINTERVALLIST" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + + test("test_gatk4_bedtointervallist") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + input[1] = [ [ id:'dict' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap new file mode 100644 index 0000000..48c322f --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_gatk4_bedtointervallist": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "1": [ + "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "versions": [ + "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T14:20:12.168775" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml new file mode 100644 index 0000000..b4d54f1 --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/bedtointervallist: + - "modules/nf-core/gatk4/bedtointervallist/**" diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md new file mode 100644 index 0000000..c6a4545 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md @@ -0,0 +1,9 @@ +# Conda is not supported at the moment + +The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) + +Hence, we are using the docker container provided by the authors of the tool: + +- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) + +This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/germlinecnvcaller/README.md b/modules/nf-core/gatk4/germlinecnvcaller/README.md new file mode 100644 index 0000000..c6a4545 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/README.md @@ -0,0 +1,9 @@ +# Conda is not supported at the moment + +The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) + +Hence, we are using the docker container provided by the authors of the tool: + +- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) + +This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test new file mode 100644 index 0000000..ee99a54 --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test @@ -0,0 +1,105 @@ +// nf-core modules test gatk4/indexfeaturefile +nextflow_process { + + name "Test Process GATK4_INDEXFEATUREFILE" + script "../main.nf" + process "GATK4_INDEXFEATUREFILE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/indexfeaturefile" + + test("test_gatk4_indexfeaturefile_bed") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("geneome.bed.idx") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_bed_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("genome.bed.gz.tbi") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("test.genome.vcf.idx") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_vcf_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("test.genome.vcf.gz.tbi") }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap new file mode 100644 index 0000000..fc19333 --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -0,0 +1,132 @@ +{ + "genome.bed.gz.tbi": { + "content": [ + "genome.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:03.068725" + }, + "test_gatk4_indexfeaturefile_vcf": { + "content": [ + [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:20.602472" + }, + "geneome.bed.idx": { + "content": [ + "genome.bed.idx" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:56:46.988441" + }, + "test.genome.vcf.gz.tbi": { + "content": [ + "test.genome.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:51.898472" + }, + "test_gatk4_indexfeaturefile_bed_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.bed.gz.tbi:md5,4bc51e2351a6e83f20e13be75861f941" + ] + ], + "1": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ], + "index": [ + [ + { + "id": "test" + }, + "genome.bed.gz.tbi:md5,4bc51e2351a6e83f20e13be75861f941" + ] + ], + "versions": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:03.058351" + }, + "test_gatk4_indexfeaturefile_vcf_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.genome.vcf.gz.tbi:md5,fedd68eaddf8d31257853d9da8325bd3" + ] + ], + "1": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ], + "index": [ + [ + { + "id": "test" + }, + "test.genome.vcf.gz.tbi:md5,fedd68eaddf8d31257853d9da8325bd3" + ] + ], + "versions": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:51.861697" + }, + "test.genome.vcf.idx": { + "content": [ + "test.genome.vcf.idx" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:20.624337" + }, + "test_gatk4_indexfeaturefile_bed": { + "content": [ + [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:56:46.885162" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml b/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml new file mode 100644 index 0000000..041bd3d --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/indexfeaturefile: + - "modules/nf-core/gatk4/indexfeaturefile/**" diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test new file mode 100644 index 0000000..2891bf9 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test @@ -0,0 +1,72 @@ +nextflow_process { + + name "Test Process GATK4_INTERVALLISTTOOLS" + script "../main.nf" + process "GATK4_INTERVALLISTTOOLS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + tag "gatk4/intervallisttools" + + setup { + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)] + ] + input[1] = [ + [ id:'dict' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + ] + """ + } + } + } + + test("test_gatk4_intervallisttools") { + + when { + process { + """ + input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("test_gatk4_intervallisttools -stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap new file mode 100644 index 0000000..7718ed0 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -0,0 +1,88 @@ +{ + "test_gatk4_intervallisttools": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995", + "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5", + "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53", + "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498" + ] + ] + ], + "1": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ], + "interval_list": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995", + "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5", + "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53", + "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498" + ] + ] + ], + "versions": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T21:26:22.252885" + }, + "test_gatk4_intervallisttools -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ], + "interval_list": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:15:11.772344" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config new file mode 100644 index 0000000..b24b20d --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_INTERVALLISTTOOLS { + ext.args = '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true' + } +} diff --git a/modules/nf-core/gatk4/intervallisttools/tests/tags.yml b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml new file mode 100644 index 0000000..bf85ff5 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/intervallisttools: + - "modules/nf-core/gatk4/intervallisttools/**" diff --git a/modules/nf-core/gatk4/mutect2/tests/f1r2.config b/modules/nf-core/gatk4/mutect2/tests/f1r2.config new file mode 100644 index 0000000..2d3c8a1 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/f1r2.config @@ -0,0 +1,3 @@ +process { + ext.args = { "--normal-sample $meta.normal_id --f1r2-tar-gz ${meta.id}.f1r2.tar.gz" } +} diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test b/modules/nf-core/gatk4/mutect2/tests/main.nf.test new file mode 100644 index 0000000..d247ee3 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test @@ -0,0 +1,360 @@ +nextflow_process { + + name "Test Process GATK4_MUTECT2" + script "../main.nf" + process "GATK4_MUTECT2" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/mutect2" + + test("tumor_normal_pair") { + config "./pair.config" + when { + process { + """ + input[0] = [ + [ + id:'test', + normal_id:'normal', + tumor_id:'tumour' + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true) + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) + ], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + input[6] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) + input[7] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.versions, + ).match() + } + ) + } + } + + test("tumor_normal_pair_f1r2") { + config "./f1r2.config" + when { + process { + """ + input[0] = [ + [ + id:'test', + normal_id:'normal', + tumor_id:'tumour' + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true) + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) + ], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + input[6] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) + input[7] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2.collect { file(it[1]).getName() }, + process.out.versions + ).match() + } + ) + } + } + test("tumor_single"){ + when { + process { + """ + input[0] = [ + [ id:'test'], + [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + input[6] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) + input[7] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.versions + ).match() + } + ) + } + } + test("cram_input"){ + when { + process{ + """ + input[0] = [ + [ id:'test'], + [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + input[6] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) + input[7] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.versions + ).match() + } + ) + } + } + + test("generate_pon") { + when { + process { + """ + input[0] = [ + [ id:'test'], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = [] + input[5] = [] + input[6] = [] + input[7] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.versions + ).match() + } + ) + } + } + + test("mitochondria"){ + when { + process { + """ + input[0] = [ + [ id:'test'], + [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + ] + input[4] = [] + input[5] = [] + input[6] = [] + input[7] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.versions + ).match() + } + ) + } + } + + test("tumor_normal_pair_f1r2_stubs"){ + options "-stub-run" + when { + process { + """ + input[0] = [ + [ + id:'test', + normal_id:'normal', + tumor_id:'tumour' + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true) + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) + ], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + ] + input[4] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + input[6] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) + input[7] = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + process.out.vcf.collect { file(it[1]).getName() }, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats.collect { file(it[1]).getName() }, + process.out.f1r2.collect { file(it[1]).getName() }, + process.out.versions.collect { file(it[1]).getName() } + ).match() + } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap new file mode 100644 index 0000000..f047af1 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -0,0 +1,204 @@ +{ + "tumor_normal_pair_f1r2_stubs": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + "test.vcf.gz.stats" + ], + [ + "test.f1r2.tar.gz" + ], + [ + "h" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-21T10:14:45.599103891" + }, + "generate_pon": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,b569ce66bbffe9588b3d221e821023ee" + ] + ], + [ + + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-20T15:57:18.264453766" + }, + "mitochondria": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,4f77301a125913170b8e9e7828b4ca3f" + ] + ], + [ + + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-20T16:05:47.668766905" + }, + "cram_input": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d" + ] + ], + [ + + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-20T15:52:27.894730554" + }, + "tumor_single": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,55ed641e16089afb33cdbc478e202d3d" + ] + ], + [ + + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-20T15:43:28.935723443" + }, + "tumor_normal_pair": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6" + ] + ], + [ + + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-20T15:31:31.913366311" + }, + "tumor_normal_pair_f1r2": { + "content": [ + [ + "test.vcf.gz" + ], + [ + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6" + ] + ], + [ + "test.f1r2.tar.gz" + ], + [ + "versions.yml:md5,d94731c50c20569fe9896235a843f382" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-03-21T09:45:52.321385704" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/mutect2/tests/mito.config b/modules/nf-core/gatk4/mutect2/tests/mito.config new file mode 100644 index 0000000..de61d3e --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/mito.config @@ -0,0 +1,3 @@ +process { + ext.args = { "--mitochondria-mode" } +} diff --git a/modules/nf-core/gatk4/mutect2/tests/pair.config b/modules/nf-core/gatk4/mutect2/tests/pair.config new file mode 100644 index 0000000..2a812b8 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/pair.config @@ -0,0 +1,3 @@ +process { + ext.args = { "--normal-sample $meta.normal_id" } +} diff --git a/modules/nf-core/gatk4/mutect2/tests/tags.yml b/modules/nf-core/gatk4/mutect2/tests/tags.yml new file mode 100644 index 0000000..4618792 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/mutect2: + - "modules/nf-core/gatk4/mutect2/**" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 0000000..17244ef --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 0000000..3223b72 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:14.779784761" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:20.256633877" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:25.632577273" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:31.058424849" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:36.479929617" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 0000000..f76a3ba --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 0000000..33ebbd5 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 0000000..e4a8394 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/tests/pipeline/cnvkit.nf.test.snap b/tests/pipeline/cnvkit.nf.test.snap index 7228c6b..15ffc8e 100644 --- a/tests/pipeline/cnvkit.nf.test.snap +++ b/tests/pipeline/cnvkit.nf.test.snap @@ -3,16 +3,24 @@ "content": [ "{CNVKIT_BATCH={cnvkit=0.9.10}, Workflow={nf-core/createpanelrefs=v1.0dev}}" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-21T12:34:52.978702536" }, "cnvkit": { "content": [ - "panel.cnn:md5,07dea67088da689ad04012552c606882", - "test.paired_end.sorted.antitargetcoverage.cnn:md5,203caf8cef6935bb50b4138097955cb8", - "test.paired_end.sorted.targetcoverage.cnn:md5,ff526714696aa49bdc1dc8d00d965266", - "test2.paired_end.sorted.antitargetcoverage.cnn:md5,203caf8cef6935bb50b4138097955cb8", - "test2.paired_end.sorted.targetcoverage.cnn:md5,6ae6b3fce7299eedca6133d911c38fe1" + "panel.cnn:md5,68028cd2b4e0fc4489bf5bfd0a73440f", + "test.paired_end.recalibrated.sorted.antitargetcoverage.cnn:md5,203caf8cef6935bb50b4138097955cb8", + "test.paired_end.recalibrated.sorted.targetcoverage.cnn:md5,0067cc3a0e479b23ab3bf056cead31b4", + "test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn:md5,203caf8cef6935bb50b4138097955cb8", + "test2.paired_end.recalibrated.sorted.targetcoverage.cnn:md5,1e1012812eb893afd931485cb760294e" ], - "timestamp": "2023-07-08T16:51:32+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-11T16:44:31.390826495" } } \ No newline at end of file diff --git a/tests/test_assets/gens_software_versions.yaml b/tests/test_assets/gens_software_versions.yaml index 9fec793..b9adcb7 100644 --- a/tests/test_assets/gens_software_versions.yaml +++ b/tests/test_assets/gens_software_versions.yaml @@ -1,12 +1,12 @@ "GENS_PON:SAMTOOLS_INDEX": - samtools: 1.18 + samtools: 1.20 "GENS_PON:GATK4_COLLECTREADCOUNTS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GENS_PON:SAMTOOLS_FAIDX": - samtools: 1.18 + samtools: 1.20 "GENS_PON:GATK4_PREPROCESSINTERVALS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GENS_PON:PICARD_CREATESEQUENCEDICTIONARY": picard: 3.1.1 "GENS_PON:GATK4_CREATEREADCOUNTPANELOFNORMALS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 diff --git a/tests/test_assets/germlinecnvcaller_software_versions.yaml b/tests/test_assets/germlinecnvcaller_software_versions.yaml index 9d9a027..cc07404 100644 --- a/tests/test_assets/germlinecnvcaller_software_versions.yaml +++ b/tests/test_assets/germlinecnvcaller_software_versions.yaml @@ -1,20 +1,20 @@ "GERMLINECNVCALLER_COHORT:GATK4_FILTERINTERVALS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_COLLECTREADCOUNTS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_GERMLINECNVCALLER": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_DETERMINEGERMLINECONTIGPLOIDY": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_ANNOTATEINTERVALS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_INTERVALLISTTOOLS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:GATK4_PREPROCESSINTERVALS": - gatk4: 4.4.0.0 + gatk4: 4.5.0.0 "GERMLINECNVCALLER_COHORT:SAMTOOLS_FAIDX": - samtools: 1.18 + samtools: 1.20 "GERMLINECNVCALLER_COHORT:SAMTOOLS_INDEX": - samtools: 1.18 + samtools: 1.20 "GERMLINECNVCALLER_COHORT:PICARD_CREATESEQUENCEDICTIONARY": picard: 3.1.1