diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b6ba322..9750a7f 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -139,28 +139,28 @@ docker-run: variables: NF_BEFORE_SCRIPT: "wget -q -O demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-methyl/demo_data.tar.gz && tar -xzvf demo_data.tar.gz" NF_PROCESS_FILES: "workflows/methyl.nf" - NF_IGNORE_PROCESSES: "index_ref_gzi,mapula,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,compress_bed,modkit,modkit_phase" + NF_IGNORE_PROCESSES: "index_ref_gzi,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,compress_bed,modkit,modkit_phase" NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bam demo_data/demo.ucram --ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001" - if: $MATRIX_NAME == "gzref-bam-mod-hap" variables: NF_BEFORE_SCRIPT: "wget -q -O demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-methyl/demo_data.tar.gz && tar -xzvf demo_data.tar.gz" NF_PROCESS_FILES: "workflows/methyl.nf" - NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,mapula,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit" + NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit" NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bam demo_data/demo.cram --ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --phased --annotation false" - if: $MATRIX_NAME == "gzref-bam-mod" variables: NF_BEFORE_SCRIPT: "wget -q -O demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-methyl/demo_data.tar.gz && tar -xzvf demo_data.tar.gz" NF_PROCESS_FILES: "workflows/methyl.nf" - NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,mapula,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit_phase" + NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,annotate_vcf,eval_downsampling,downsampling,modkit_phase" NF_WORKFLOW_OPTS: "--snp false --sv false --mod --cnv false --str false --bam demo_data/demo.cram --ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 --ubam_bam2fq_threads 1 --bam_min_coverage 0.00001 --annotation false" - if: $MATRIX_NAME == "downsample" variables: NF_BEFORE_SCRIPT: "wget -qO demo_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-human-str/demo_data.tar.gz && tar -xzvf demo_data.tar.gz" NF_PROCESS_FILES: "workflows/methyl.nf" - NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,mapula,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,eval_downsampling,downsampling,compress_bed,modkit_phase,annotate_vcf" + NF_IGNORE_PROCESSES: "minimap2_ubam,index_ref_gzi,getGenome,get_coverage,getVersions,getParams,failedQCReport,makeAlignmentReport,eval_downsampling,downsampling,compress_bed,modkit_phase,annotate_vcf" NF_WORKFLOW_OPTS: "--snp false --sv false --mod --annotation false --bam demo_data/demo.bam --ref demo_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa.gz \ --sample_name HOOT --ubam_map_threads 2 --ubam_sort_threads 1 \ --ubam_bam2fq_threads 1 --bam_min_coverage 0 --skip_annotation \ diff --git a/CHANGELOG.md b/CHANGELOG.md index 615477d..1103316 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - wf-basecalling subworkflow - fast5_dir input and other basecalling related options have been removed from the workflow parameters - Users should run the standalone wf-basecalling workflow and provide the output to wf-human-variation +- Mapula statistics with `--mapula` ## [v1.9.2] ### Fixed diff --git a/main.nf b/main.nf index 533b9a3..424b2e5 100755 --- a/main.nf +++ b/main.nf @@ -23,7 +23,6 @@ include { mosdepth as mosdepth_input; mosdepth as mosdepth_downsampled; readStats; - mapula; getAllChromosomesBed; publish_artifact; configure_jbrowse; @@ -217,14 +216,6 @@ workflow { } else { mosdepth_perbase = Channel.from("$projectDir/data/OPTIONAL_FILE") } - - if (params.mapula) { - mapula(bam_channel, bed, ref_channel) - mapula_stats = mapula.out - } - else { - mapula_stats = Channel.empty() - } // Determine if the coverage threshold is met to perform analysis. // If too low, it creates an empty input channel, @@ -619,7 +610,6 @@ workflow { mosdepth_summary.flatten(), mosdepth_perbase.flatten(), mod_stats.flatten(), - mapula_stats.flatten(), jb_conf.flatten(), report_pass.flatten(), report_fail.flatten(), diff --git a/modules/local/common.nf b/modules/local/common.nf index 27b6771..9c6a332 100755 --- a/modules/local/common.nf +++ b/modules/local/common.nf @@ -96,26 +96,6 @@ process mosdepth { } -process mapula { - cpus 1 - memory { 4.GB * task.attempt } - maxRetries 2 - errorStrategy = {task.exitStatus in [137,140] ? 'retry' : 'finish'} - input: - tuple path(xam), path(xam_idx), val(xam_meta) - path target_bed - tuple path(ref), path(ref_idx), path(ref_cache), env(REF_PATH) - output: - tuple \ - path("${params.sample_name}.mapula.csv"), - path("${params.sample_name}.mapula.json") - script: - """ - mapula count -r ${ref} -f all -n '${params.sample_name}.mapula' ${xam} - """ -} - - process readStats { label "wf_common" cpus 4 diff --git a/nextflow.config b/nextflow.config index 430d2a2..f38fe1f 100755 --- a/nextflow.config +++ b/nextflow.config @@ -29,7 +29,6 @@ params { mod = false cnv = false str = false - mapula = false // slow, should be deprecated // benchmark feature flags sv_benchmark = false @@ -115,7 +114,7 @@ params { template_version = "195cab5" example_cmd = [ "--bam 'wf-human-variation-demo/demo.bam'", - "--basecaller_cfg 'clair3:dna_r10.4.1_e8.2_400bps_hac_prom'", + "--basecaller_cfg 'dna_r10.4.1_e8.2_400bps_hac_prom'", "--mod", "--ref 'wf-human-variation-demo/demo.fasta'", "--sample_name 'DEMO'", @@ -125,7 +124,7 @@ params { agent = null // container sha - e2l_base_tag = "sha0800eade05e4cbb75d45421633c78c4f6320b2f6" + e2l_base_tag = "sha26be394971f6444d657b0be6745a341beb0b2843" e2l_snp_tag = "sha14d7c4b75950fbffae7b2ea452dba21b263b84a1" e2l_sv_tag = "shabc3ac908a14705f248cdf49f218956ec33e93ef9" e2l_mod_tag = "shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb" @@ -228,7 +227,7 @@ profiles { queue = { "${params.aws_queue}" } memory = '8G' withLabel:wfdefault { - container = { "${params.aws_image_prefix}-${params.wf.name}:${params.wf.e2l_base_tag}-root" } + container = { "${params.aws_image_prefix}-${params.wf.name}:${params.wf.e2l_base_tag}" } } withLabel:wf_human_snp { container = { "${params.aws_image_prefix}-wf-human-variation-snp:${params.wf.e2l_snp_tag}-root" } diff --git a/nextflow_schema.json b/nextflow_schema.json index ad2d529..995e9dc 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -49,13 +49,6 @@ "description": "Enable output of modified calls to a bedMethyl file [requires input BAM with Ml and Mm tags]", "help_text": "This option is automatically selected and aggregation of modified calls with be carried out using modkit if Ml and Mm tags are found. Disable this option to prevent output of a bedMethyl file.", "default": false - }, - "mapula": { - "type": "boolean", - "description": "Enable mapula to generate basic alignment QC statistics (can be slow on very large data sets)", - "help_text": "Mapula is a tool that is able to parse alignments and produce a range of useful stats. In most cases the other outputs are sufficient and this does not need to be enabled.", - "hidden": true, - "default": false } }, "anyOf": [