diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml index ed1198d8260..1f5deb375a8 100644 --- a/modules/nf-core/mirtop/counts/environment.yml +++ b/modules/nf-core/mirtop/counts/environment.yml @@ -4,6 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf index 9b623bff8f3..a4ca1889fb1 100644 --- a/modules/nf-core/mirtop/counts/main.nf +++ b/modules/nf-core/mirtop/counts/main.nf @@ -3,9 +3,7 @@ process MIRTOP_COUNTS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test index 52b31db1eb2..5048c166ab8 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -54,12 +54,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions - ).match() - }, - // md5sum is not stable, order of elements in column "variant" change - { assert file(process.out.tsv[0][1]).readLines().findAll { it.contains("iso-22-I0S21NSLN") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap index d05798b0bb6..104acf131db 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ], "tsv": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ] } ], @@ -30,18 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T13:24:41.148536938" + "timestamp": "2024-09-18T15:05:22.556134542" }, "isomir - bam": { "content": [ - [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "1": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ], + "tsv": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "versions": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T18:39:50.607483472" + "timestamp": "2024-09-18T16:05:58.332523272" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml index 4b5ae03a45a..17572707529 100644 --- a/modules/nf-core/mirtop/export/environment.yml +++ b/modules/nf-core/mirtop/export/environment.yml @@ -1,10 +1,11 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/export/main.nf b/modules/nf-core/mirtop/export/main.nf index 33f6c303262..b99333def69 100644 --- a/modules/nf-core/mirtop/export/main.nf +++ b/modules/nf-core/mirtop/export/main.nf @@ -3,9 +3,7 @@ process MIRTOP_EXPORT { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap index f8c668a62fb..ea272199f4a 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/export/tests/main.nf.test.snap @@ -22,7 +22,7 @@ ] ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ [ @@ -44,7 +44,7 @@ ] ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -52,7 +52,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T15:25:40.531010949" + "timestamp": "2024-09-18T14:54:17.653801164" }, "isomir - bam": { "content": [ @@ -72,7 +72,7 @@ ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ @@ -89,7 +89,7 @@ ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -97,6 +97,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:12:49.612315132" + "timestamp": "2024-09-18T16:06:37.626754369" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml index 6e57308ae1c..1f5deb375a8 100644 --- a/modules/nf-core/mirtop/gff/environment.yml +++ b/modules/nf-core/mirtop/gff/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf index 453b624b9f6..aeb26bcc64a 100644 --- a/modules/nf-core/mirtop/gff/main.nf +++ b/modules/nf-core/mirtop/gff/main.nf @@ -3,9 +3,7 @@ process MIRTOP_GFF { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(bam, arity:'1..*') @@ -14,7 +12,7 @@ process MIRTOP_GFF { output: tuple val(meta), path("mirtop/*mirtop.gff") , emit: gff - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test index 3ce7ef85523..85977b43665 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -33,13 +33,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.bam, - process.out.versions, - ).match() - }, - // md5sum is not stable, order of elements in section "variant" may change - { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap index a9e6f852e6f..0dddae2d318 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ], "gff": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ] } ], @@ -30,19 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:40:30.542921953" + "timestamp": "2024-09-18T14:31:04.976117723" }, "isomir - bam": { "content": [ - null, - [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "1": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ], + "gff": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "versions": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:38:09.903017316" + "timestamp": "2024-09-18T16:07:04.203181613" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml index 3c24c43e805..1f5deb375a8 100644 --- a/modules/nf-core/mirtop/stats/environment.yml +++ b/modules/nf-core/mirtop/stats/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::pandas=1.3.5" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/stats/main.nf b/modules/nf-core/mirtop/stats/main.nf index 51d33019a99..4742448b8c1 100644 --- a/modules/nf-core/mirtop/stats/main.nf +++ b/modules/nf-core/mirtop/stats/main.nf @@ -4,9 +4,7 @@ process MIRTOP_STATS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap index ba9633d12a2..2904830d59e 100644 --- a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:49:32.73944037" + "timestamp": "2024-09-18T15:02:00.325615537" }, "isomir - bam": { "content": [ @@ -56,7 +56,7 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "1": [ @@ -64,18 +64,18 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "txt": [ @@ -83,11 +83,11 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -95,6 +95,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:47:39.121648755" + "timestamp": "2024-09-18T15:01:49.621322368" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap index 2a0e41a3439..513f11be483 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap @@ -14,7 +14,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.txt:md5,e89c014047ffffed65f1ec4fb328e3bc" + "mirtop_stats.txt:md5,3db542a532cf3f3c8b4efda134bd6202" ] ], [ @@ -22,20 +22,20 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.log:md5,49b85517828253858cc60a0390567585" + "mirtop_stats.log:md5,676d0cedfb4770f7862bc0601c2a7f15" ] ], [ - "versions.yml:md5,04fed9539a0164a116d37bf090613d42", - "versions.yml:md5,13a50e3cef16f8bb981197bbc9a46d8e", - "versions.yml:md5,5f6bea8a46cdfec82b3d8f1b6c906ac7", - "versions.yml:md5,976382d50b05cded89483e2415fde415" + "versions.yml:md5,60caed2a2383e82ed06867a75d5a50e2", + "versions.yml:md5,87d473a6cb931a2032357c3272b3249d", + "versions.yml:md5,91c635a35016586e75b620c7f33e6461", + "versions.yml:md5,b314282e0db6b00dc8acaffe182f2b80" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:13:48.308574263" + "timestamp": "2024-09-19T21:09:04.079276367" } } \ No newline at end of file