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bump samtools #6648

Merged
merged 15 commits into from
Sep 18, 2024
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/ampliconclip/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
- bioconda::samtools=1.21
- bioconda::htslib=1.21
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/ampliconclip/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_AMPLICONCLIP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(bam)
Expand Down
104 changes: 52 additions & 52 deletions modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
@@ -1,75 +1,45 @@
{
"bam_bed_versions": {
"content": [
[
"versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-05-28T15:43:25.843761003"
},
"bam_bed_stats": {
"bam_bed_save_all_versions": {
"content": [
[

"versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.3"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-02T13:43:02.239309"
"timestamp": "2024-09-16T07:45:31.382344883"
},
"bam_bed_save_all_stats": {
"bam_bed_save_all_rejects_bam": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a"
"test.cliprejects.bam:md5,8aa0f82e1c2dbfd9fcfab0fe3efa0ada"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.04.3"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-02-02T13:43:14.110481"
"timestamp": "2024-09-16T07:45:31.334527155"
},
"bam_bed_save_all_versions": {
"bam_bed_versions": {
"content": [
[
"versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
"versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:43:36.405710677"
},
"bam_bed_save_all_rejects_bam": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test.cliprejects.bam:md5,e3c76daf46d83b2327a1168170b08fca"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-05-28T15:43:36.39935122"
"timestamp": "2024-09-16T07:45:11.300085385"
},
"bam_bed_save_clipsats_name": {
"content": [
Expand Down Expand Up @@ -99,15 +69,27 @@
"id": "test",
"single_end": false
},
"test.cliprejects.bam:md5,f29869fea697a5041f588970d9cf2392"
"test.cliprejects.bam:md5,9d0caf53bd9a8ccb4a5ce60393635ee0"
]
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-16T07:45:21.573836864"
},
"bam_bed_stats": {
"content": [
[

]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "23.04.3"
},
"timestamp": "2024-05-28T15:43:31.133760457"
"timestamp": "2024-02-02T13:43:02.239309"
},
"bam_bed_save_clipsats_stats": {
"content": [
Expand All @@ -121,17 +103,35 @@
},
"timestamp": "2024-02-13T16:13:25.207756781"
},
"bam_bed_save_clipsats_versions": {
"bam_bed_save_all_stats": {
"content": [
[
"versions.yml:md5,377f547954102b9f96e37c8add7b2e4d"
[
{
"id": "test",
"single_end": false
},
"test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a"
]
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "23.04.3"
},
"timestamp": "2024-02-02T13:43:14.110481"
},
"bam_bed_save_clipsats_versions": {
"content": [
[
"versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:43:31.138774495"
"timestamp": "2024-09-16T07:45:21.620404522"
},
"bam_bed_save_all_name": {
"content": [
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/bam2fq/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
- bioconda::samtools=1.21
- bioconda::htslib=1.21
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/bam2fq/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(inputbam)
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -51,25 +51,25 @@
"bam_versions": {
"content": [
[
"versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
"versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:43:52.415053401"
"timestamp": "2024-09-16T07:46:07.695175929"
},
"bam_split_versions": {
"content": [
[
"versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
"versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:43:57.740193087"
"timestamp": "2024-09-16T07:46:17.91793415"
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/calmd/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
- bioconda::samtools=1.21
- bioconda::htslib=1.21
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/calmd/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_CALMD {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(bam)
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/samtools/calmd/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -22,25 +22,25 @@
"bam_stub_versions": {
"content": [
[
"versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd"
"versions.yml:md5,6082f9d3311ea0138839acc5341c115f"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:42:47.344537089"
"timestamp": "2024-09-16T07:47:04.212973938"
},
"bam_versions": {
"content": [
[
"versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd"
"versions.yml:md5,6082f9d3311ea0138839acc5341c115f"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:42:41.963108136"
"timestamp": "2024-09-16T07:46:53.00613089"
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/cat/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
- bioconda::samtools=1.21
- bioconda::htslib=1.21
5 changes: 2 additions & 3 deletions modules/nf-core/samtools/cat/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_CAT {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(input_files, stageAs: "?/*")
Expand All @@ -26,7 +26,6 @@ process SAMTOOLS_CAT {
"""
samtools \\
cat \\
--threads ${task.cpus-1} \\
$args \\
-o ${prefix}.${file_type} \\
$input_files
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/samtools/cat/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,14 @@
"bams_stub_versions": {
"content": [
[
"versions.yml:md5,9b9451947b5de303ed028cf6513be3e8"
"versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:45:35.044644556"
"timestamp": "2024-09-16T07:47:51.511914861"
},
"bams_bam": {
"content": [
Expand Down Expand Up @@ -58,13 +58,13 @@
"bams_versions": {
"content": [
[
"versions.yml:md5,9b9451947b5de303ed028cf6513be3e8"
"versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-28T15:45:29.652817652"
"timestamp": "2024-09-16T08:47:50.783194958"
}
}
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/collate/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
- bioconda::samtools=1.21
- bioconda::htslib=1.21
4 changes: 2 additions & 2 deletions modules/nf-core/samtools/collate/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process SAMTOOLS_COLLATE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0':
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0':
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(input)
Expand Down
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