From 0dee12b56ccecc416d6f7a1ccd85fd571eab3307 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 10 Jul 2024 14:28:29 +0200 Subject: [PATCH] chore: bump picard (#5948) * bump picard * fix hsmetrics test * fix markduplicates * fix extractfingerprints * fix addorreplacereadgroups * fix crosscheckfingerprints --- .../addorreplacereadgroups/environment.yml | 2 +- .../picard/addorreplacereadgroups/main.nf | 4 +- .../tests/main.nf.test.snap | 20 +- .../picard/bedtointervallist/environment.yml | 2 +- .../nf-core/picard/bedtointervallist/main.nf | 4 +- .../nf-core/picard/cleansam/environment.yml | 2 +- modules/nf-core/picard/cleansam/main.nf | 4 +- .../picard/collecthsmetrics/environment.yml | 2 +- .../nf-core/picard/collecthsmetrics/main.nf | 4 +- .../collecthsmetrics/tests/main.nf.test | 8 +- .../collecthsmetrics/tests/main.nf.test.snap | 502 +----------------- .../collectinsertsizemetrics/environment.yml | 2 +- .../picard/collectinsertsizemetrics/main.nf | 4 +- .../collectmultiplemetrics/environment.yml | 2 +- .../picard/collectmultiplemetrics/main.nf | 4 +- .../collectrnaseqmetrics/environment.yml | 2 +- .../picard/collectrnaseqmetrics/main.nf | 4 +- .../picard/collectwgsmetrics/environment.yml | 2 +- .../nf-core/picard/collectwgsmetrics/main.nf | 4 +- .../createsequencedictionary/environment.yml | 2 +- .../picard/createsequencedictionary/main.nf | 4 +- .../crosscheckfingerprints/environment.yml | 2 +- .../picard/crosscheckfingerprints/main.nf | 4 +- .../tests/main.nf.test.snap | 12 +- .../picard/extractfingerprint/environment.yml | 2 +- .../nf-core/picard/extractfingerprint/main.nf | 4 +- .../tests/main.nf.test.snap | 12 +- .../nf-core/picard/fastqtosam/environment.yml | 2 +- modules/nf-core/picard/fastqtosam/main.nf | 4 +- .../picard/filtersamreads/environment.yml | 2 +- modules/nf-core/picard/filtersamreads/main.nf | 4 +- .../picard/fixmateinformation/environment.yml | 2 +- .../nf-core/picard/fixmateinformation/main.nf | 4 +- .../picard/liftovervcf/environment.yml | 2 +- modules/nf-core/picard/liftovervcf/main.nf | 4 +- .../picard/markduplicates/environment.yml | 2 +- modules/nf-core/picard/markduplicates/main.nf | 4 +- .../markduplicates/tests/main.nf.test.snap | 36 +- .../picard/mergesamfiles/environment.yml | 2 +- modules/nf-core/picard/mergesamfiles/main.nf | 4 +- .../picard/renamesampleinvcf/environment.yml | 2 +- .../nf-core/picard/renamesampleinvcf/main.nf | 4 +- .../scatterintervalsbyns/environment.yml | 2 +- .../picard/scatterintervalsbyns/main.nf | 4 +- .../nf-core/picard/sortsam/environment.yml | 2 +- modules/nf-core/picard/sortsam/main.nf | 4 +- .../nf-core/picard/sortvcf/environment.yml | 2 +- modules/nf-core/picard/sortvcf/main.nf | 4 +- .../tests/main.nf.test.snap | 26 +- .../bam_qc_picard/tests/main.nf.test.snap | 16 +- 50 files changed, 159 insertions(+), 599 deletions(-) diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index d7d2c6c0317..5c6ba553074 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 4300ba7f8cf..3f03c6808a5 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index 63a55843cee..f823197d284 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.replaced.cram", [ - "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-21T12:05:47.668865" + "timestamp": "2024-07-10T09:54:40.471730168" }, "sarscov2 - bam - stub": { "content": [ @@ -30,7 +30,7 @@ ], "3": [ - "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" ], "bai": [ @@ -47,28 +47,28 @@ ], "versions": [ - "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-21T10:51:24.530553" + "timestamp": "2024-07-10T09:55:08.402649243" }, "sarscov2 - bam": { "content": [ "null.replaced.bam", "null.replaced.bai", [ - "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891" + "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-21T12:05:29.696728" + "timestamp": "2024-07-10T09:54:22.239968953" } } \ No newline at end of file diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml index 57368ccf754..1d12dbf858b 100644 --- a/modules/nf-core/picard/bedtointervallist/environment.yml +++ b/modules/nf-core/picard/bedtointervallist/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf index 099d07d183a..2cc6cbd2f0f 100644 --- a/modules/nf-core/picard/bedtointervallist/main.nf +++ b/modules/nf-core/picard/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta) , path(bed) diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml index c48cabe0ec6..0f00fd740ed 100644 --- a/modules/nf-core/picard/cleansam/environment.yml +++ b/modules/nf-core/picard/cleansam/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 4f6a91f17c4..7b95cebdc0f 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -4,8 +4,8 @@ process PICARD_CLEANSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index fbeab71bb90..b00842b1b73 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 1e80b529782..a9cbafd44f2 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 3d0575b395a..94713c0f965 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { then { def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..212] + def lines = path(process.out.metrics[0][1]).readLines()[0..100] lines.remove(3) // remove timestamp assertAll( { assert process.success }, @@ -97,7 +97,7 @@ nextflow_process { then { def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..212] + def lines = path(process.out.metrics[0][1]).readLines()[0..100] lines.remove(3) // remove timestamp assertAll( { assert process.success }, @@ -135,7 +135,7 @@ nextflow_process { then { def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..212] + def lines = path(process.out.metrics[0][1]).readLines()[0..100] lines.remove(3) // remove timestamp assertAll( { assert process.success }, @@ -173,7 +173,7 @@ nextflow_process { then { def size = path(process.out.metrics[0][1]).size() - def lines = path(process.out.metrics[0][1]).readLines()[0..212] + def lines = path(process.out.metrics[0][1]).readLines()[0..100] lines.remove(3) // remove timestamp assertAll( { assert process.success }, diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index b3b477e1f01..53855d13b68 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - bam - nofasta": { "content": [ "test.CollectHsMetrics.coverage_metrics", - 4140, + 3548, [ "## htsjdk.samtools.metrics.StringHeader", "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", @@ -10,7 +10,7 @@ "", "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.016027\t0\t\t\t", + "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t", "", "## HISTOGRAM\tjava.lang.Integer", "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", @@ -103,146 +103,34 @@ "86\t0\t0", "87\t0\t0", "88\t0\t0", - "89\t0\t0", - "90\t0\t0", - "91\t0\t0", - "92\t0\t0", - "93\t0\t0", - "94\t0\t0", - "95\t0\t0", - "96\t0\t0", - "97\t0\t0", - "98\t0\t0", - "99\t0\t0", - "100\t0\t0", - "101\t0\t0", - "102\t0\t0", - "103\t0\t0", - "104\t0\t0", - "105\t0\t0", - "106\t0\t0", - "107\t0\t0", - "108\t0\t0", - "109\t0\t0", - "110\t0\t0", - "111\t0\t0", - "112\t0\t0", - "113\t0\t0", - "114\t0\t0", - "115\t0\t0", - "116\t0\t0", - "117\t0\t0", - "118\t0\t0", - "119\t0\t0", - "120\t0\t0", - "121\t0\t0", - "122\t0\t0", - "123\t0\t0", - "124\t0\t0", - "125\t0\t0", - "126\t0\t0", - "127\t0\t0", - "128\t0\t0", - "129\t0\t0", - "130\t0\t0", - "131\t0\t0", - "132\t0\t0", - "133\t0\t0", - "134\t0\t0", - "135\t0\t0", - "136\t0\t0", - "137\t0\t0", - "138\t0\t0", - "139\t0\t0", - "140\t0\t0", - "141\t0\t0", - "142\t0\t0", - "143\t0\t0", - "144\t0\t0", - "145\t0\t0", - "146\t0\t0", - "147\t0\t0", - "148\t0\t0", - "149\t0\t0", - "150\t0\t0", - "151\t0\t0", - "152\t0\t0", - "153\t0\t0", - "154\t0\t0", - "155\t0\t0", - "156\t0\t0", - "157\t0\t0", - "158\t0\t0", - "159\t0\t0", - "160\t0\t0", - "161\t0\t0", - "162\t0\t0", - "163\t0\t0", - "164\t0\t0", - "165\t0\t0", - "166\t0\t0", - "167\t0\t0", - "168\t0\t0", - "169\t0\t0", - "170\t0\t0", - "171\t0\t0", - "172\t0\t0", - "173\t0\t0", - "174\t0\t0", - "175\t0\t0", - "176\t0\t0", - "177\t0\t0", - "178\t0\t0", - "179\t0\t0", - "180\t0\t0", - "181\t0\t0", - "182\t0\t0", - "183\t0\t0", - "184\t0\t0", - "185\t0\t0", - "186\t0\t0", - "187\t0\t0", - "188\t0\t0", - "189\t0\t0", - "190\t0\t0", - "191\t0\t0", - "192\t0\t0", - "193\t0\t0", - "194\t0\t0", - "195\t0\t0", - "196\t0\t0", - "197\t0\t0", - "198\t0\t0", - "199\t0\t0", - "200\t0\t0", - "" + "89\t0\t0" ], [ - "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d" + "versions.yml:md5,e390b048af294086f56621c38ebde05a" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-10T09:17:21.08792" + "timestamp": "2024-07-10T09:45:46.991614248" }, "versions": { "content": [ [ - "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d" + "versions.yml:md5,e390b048af294086f56621c38ebde05a" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-10T09:16:57.995147" + "timestamp": "2024-07-10T09:36:50.350567213" }, "sarscov2 - bam - samebed": { "content": [ "test.CollectHsMetrics.coverage_metrics", - 4178, + 3586, [ "## htsjdk.samtools.metrics.StringHeader", "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", @@ -250,7 +138,7 @@ "", "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394304\t2\t\t\t", + "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t", "", "## HISTOGRAM\tjava.lang.Integer", "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", @@ -343,134 +231,22 @@ "86\t0\t0", "87\t0\t0", "88\t0\t0", - "89\t0\t0", - "90\t0\t0", - "91\t0\t0", - "92\t0\t0", - "93\t0\t0", - "94\t0\t0", - "95\t0\t0", - "96\t0\t0", - "97\t0\t0", - "98\t0\t0", - "99\t0\t0", - "100\t0\t0", - "101\t0\t0", - "102\t0\t0", - "103\t0\t0", - "104\t0\t0", - "105\t0\t0", - "106\t0\t0", - "107\t0\t0", - "108\t0\t0", - "109\t0\t0", - "110\t0\t0", - "111\t0\t0", - "112\t0\t0", - "113\t0\t0", - "114\t0\t0", - "115\t0\t0", - "116\t0\t0", - "117\t0\t0", - "118\t0\t0", - "119\t0\t0", - "120\t0\t0", - "121\t0\t0", - "122\t0\t0", - "123\t0\t0", - "124\t0\t0", - "125\t0\t0", - "126\t0\t0", - "127\t0\t0", - "128\t0\t0", - "129\t0\t0", - "130\t0\t0", - "131\t0\t0", - "132\t0\t0", - "133\t0\t0", - "134\t0\t0", - "135\t0\t0", - "136\t0\t0", - "137\t0\t0", - "138\t0\t0", - "139\t0\t0", - "140\t0\t0", - "141\t0\t0", - "142\t0\t0", - "143\t0\t0", - "144\t0\t0", - "145\t0\t0", - "146\t0\t0", - "147\t0\t0", - "148\t0\t0", - "149\t0\t0", - "150\t0\t0", - "151\t0\t0", - "152\t0\t0", - "153\t0\t0", - "154\t0\t0", - "155\t0\t0", - "156\t0\t0", - "157\t0\t0", - "158\t0\t0", - "159\t0\t0", - "160\t0\t0", - "161\t0\t0", - "162\t0\t0", - "163\t0\t0", - "164\t0\t0", - "165\t0\t0", - "166\t0\t0", - "167\t0\t0", - "168\t0\t0", - "169\t0\t0", - "170\t0\t0", - "171\t0\t0", - "172\t0\t0", - "173\t0\t0", - "174\t0\t0", - "175\t0\t0", - "176\t0\t0", - "177\t0\t0", - "178\t0\t0", - "179\t0\t0", - "180\t0\t0", - "181\t0\t0", - "182\t0\t0", - "183\t0\t0", - "184\t0\t0", - "185\t0\t0", - "186\t0\t0", - "187\t0\t0", - "188\t0\t0", - "189\t0\t0", - "190\t0\t0", - "191\t0\t0", - "192\t0\t0", - "193\t0\t0", - "194\t0\t0", - "195\t0\t0", - "196\t0\t0", - "197\t0\t0", - "198\t0\t0", - "199\t0\t0", - "200\t0\t0", - "" + "89\t0\t0" ], [ - "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d" + "versions.yml:md5,e390b048af294086f56621c38ebde05a" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-10T09:18:16.259373" + "timestamp": "2024-07-10T09:46:33.770516478" }, "sarscov2 - bam": { "content": [ "test.CollectHsMetrics.coverage_metrics", - 4190, + 3598, [ "## htsjdk.samtools.metrics.StringHeader", "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", @@ -478,7 +254,7 @@ "", "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.016027\t0\t\t\t", + "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", "", "## HISTOGRAM\tjava.lang.Integer", "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", @@ -571,134 +347,22 @@ "86\t0\t0", "87\t0\t0", "88\t0\t0", - "89\t0\t0", - "90\t0\t0", - "91\t0\t0", - "92\t0\t0", - "93\t0\t0", - "94\t0\t0", - "95\t0\t0", - "96\t0\t0", - "97\t0\t0", - "98\t0\t0", - "99\t0\t0", - "100\t0\t0", - "101\t0\t0", - "102\t0\t0", - "103\t0\t0", - "104\t0\t0", - "105\t0\t0", - "106\t0\t0", - "107\t0\t0", - "108\t0\t0", - "109\t0\t0", - "110\t0\t0", - "111\t0\t0", - "112\t0\t0", - "113\t0\t0", - "114\t0\t0", - "115\t0\t0", - "116\t0\t0", - "117\t0\t0", - "118\t0\t0", - "119\t0\t0", - "120\t0\t0", - "121\t0\t0", - "122\t0\t0", - "123\t0\t0", - "124\t0\t0", - "125\t0\t0", - "126\t0\t0", - "127\t0\t0", - "128\t0\t0", - "129\t0\t0", - "130\t0\t0", - "131\t0\t0", - "132\t0\t0", - "133\t0\t0", - "134\t0\t0", - "135\t0\t0", - "136\t0\t0", - "137\t0\t0", - "138\t0\t0", - "139\t0\t0", - "140\t0\t0", - "141\t0\t0", - "142\t0\t0", - "143\t0\t0", - "144\t0\t0", - "145\t0\t0", - "146\t0\t0", - "147\t0\t0", - "148\t0\t0", - "149\t0\t0", - "150\t0\t0", - "151\t0\t0", - "152\t0\t0", - "153\t0\t0", - "154\t0\t0", - "155\t0\t0", - "156\t0\t0", - "157\t0\t0", - "158\t0\t0", - "159\t0\t0", - "160\t0\t0", - "161\t0\t0", - "162\t0\t0", - "163\t0\t0", - "164\t0\t0", - "165\t0\t0", - "166\t0\t0", - "167\t0\t0", - "168\t0\t0", - "169\t0\t0", - "170\t0\t0", - "171\t0\t0", - "172\t0\t0", - "173\t0\t0", - "174\t0\t0", - "175\t0\t0", - "176\t0\t0", - "177\t0\t0", - "178\t0\t0", - "179\t0\t0", - "180\t0\t0", - "181\t0\t0", - "182\t0\t0", - "183\t0\t0", - "184\t0\t0", - "185\t0\t0", - "186\t0\t0", - "187\t0\t0", - "188\t0\t0", - "189\t0\t0", - "190\t0\t0", - "191\t0\t0", - "192\t0\t0", - "193\t0\t0", - "194\t0\t0", - "195\t0\t0", - "196\t0\t0", - "197\t0\t0", - "198\t0\t0", - "199\t0\t0", - "200\t0\t0", - "" + "89\t0\t0" ], [ - "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d" + "versions.yml:md5,e390b048af294086f56621c38ebde05a" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-10T09:13:12.139682" + "timestamp": "2024-07-10T09:45:16.117386245" }, "sarscov2 - bam - bed": { "content": [ "test.CollectHsMetrics.coverage_metrics", - 4187, + 3595, [ "## htsjdk.samtools.metrics.StringHeader", "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", @@ -706,7 +370,7 @@ "", "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", - "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.016027\t0\t\t\t", + "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", "", "## HISTOGRAM\tjava.lang.Integer", "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", @@ -799,128 +463,16 @@ "86\t0\t0", "87\t0\t0", "88\t0\t0", - "89\t0\t0", - "90\t0\t0", - "91\t0\t0", - "92\t0\t0", - "93\t0\t0", - "94\t0\t0", - "95\t0\t0", - "96\t0\t0", - "97\t0\t0", - "98\t0\t0", - "99\t0\t0", - "100\t0\t0", - "101\t0\t0", - "102\t0\t0", - "103\t0\t0", - "104\t0\t0", - "105\t0\t0", - "106\t0\t0", - "107\t0\t0", - "108\t0\t0", - "109\t0\t0", - "110\t0\t0", - "111\t0\t0", - "112\t0\t0", - "113\t0\t0", - "114\t0\t0", - "115\t0\t0", - "116\t0\t0", - "117\t0\t0", - "118\t0\t0", - "119\t0\t0", - "120\t0\t0", - "121\t0\t0", - "122\t0\t0", - "123\t0\t0", - "124\t0\t0", - "125\t0\t0", - "126\t0\t0", - "127\t0\t0", - "128\t0\t0", - "129\t0\t0", - "130\t0\t0", - "131\t0\t0", - "132\t0\t0", - "133\t0\t0", - "134\t0\t0", - "135\t0\t0", - "136\t0\t0", - "137\t0\t0", - "138\t0\t0", - "139\t0\t0", - "140\t0\t0", - "141\t0\t0", - "142\t0\t0", - "143\t0\t0", - "144\t0\t0", - "145\t0\t0", - "146\t0\t0", - "147\t0\t0", - "148\t0\t0", - "149\t0\t0", - "150\t0\t0", - "151\t0\t0", - "152\t0\t0", - "153\t0\t0", - "154\t0\t0", - "155\t0\t0", - "156\t0\t0", - "157\t0\t0", - "158\t0\t0", - "159\t0\t0", - "160\t0\t0", - "161\t0\t0", - "162\t0\t0", - "163\t0\t0", - "164\t0\t0", - "165\t0\t0", - "166\t0\t0", - "167\t0\t0", - "168\t0\t0", - "169\t0\t0", - "170\t0\t0", - "171\t0\t0", - "172\t0\t0", - "173\t0\t0", - "174\t0\t0", - "175\t0\t0", - "176\t0\t0", - "177\t0\t0", - "178\t0\t0", - "179\t0\t0", - "180\t0\t0", - "181\t0\t0", - "182\t0\t0", - "183\t0\t0", - "184\t0\t0", - "185\t0\t0", - "186\t0\t0", - "187\t0\t0", - "188\t0\t0", - "189\t0\t0", - "190\t0\t0", - "191\t0\t0", - "192\t0\t0", - "193\t0\t0", - "194\t0\t0", - "195\t0\t0", - "196\t0\t0", - "197\t0\t0", - "198\t0\t0", - "199\t0\t0", - "200\t0\t0", - "" + "89\t0\t0" ], [ - "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d" + "versions.yml:md5,e390b048af294086f56621c38ebde05a" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-10T09:17:48.183631" + "timestamp": "2024-07-10T09:46:13.489487836" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml index 73ba7dc6bcf..87a8c7d8055 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf index 06c4bc17223..9915399269f 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf +++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index 79b33280653..6a16f00dcc6 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 5640ce9411f..c5555871dc3 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta) , path(bam), path(bai) diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml index 542b2e823fe..1dfb9654889 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf index f833a105c84..0c8f2cfa2c1 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf +++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 6a0b9258e0f..9f87553465b 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 - r::r-base diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 35f4129cfb2..6002a7ca95c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml index f3554628b84..48a31a26dcc 100644 --- a/modules/nf-core/picard/createsequencedictionary/environment.yml +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index a1eb8bed5c4..bc925a0dedc 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml index ab81a3dceb1..5df18044c3c 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index 50e0376c266..f6df55ade7b 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -4,8 +4,8 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(input1), path(input1_index), path(input2), path(input2_index), path(haplotype_map) diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap index 96fbdc845d4..f283f13305f 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap +++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap @@ -22,25 +22,25 @@ "Crosscheck versions stub": { "content": [ [ - "versions.yml:md5,bd0a3212a131aee499cb7f954aeac63c" + "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:36:24.83939" + "timestamp": "2024-07-10T09:57:33.939689662" }, "Crosscheck versions - bam": { "content": [ [ - "versions.yml:md5,bd0a3212a131aee499cb7f954aeac63c" + "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-08T14:30:50.311883" + "timestamp": "2024-07-10T09:57:08.745266455" } } \ No newline at end of file diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml index 40429b416b3..b6d7eef616c 100644 --- a/modules/nf-core/picard/extractfingerprint/environment.yml +++ b/modules/nf-core/picard/extractfingerprint/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/extractfingerprint/main.nf b/modules/nf-core/picard/extractfingerprint/main.nf index c10c3847ead..68b53233045 100644 --- a/modules/nf-core/picard/extractfingerprint/main.nf +++ b/modules/nf-core/picard/extractfingerprint/main.nf @@ -4,8 +4,8 @@ process PICARD_EXTRACTFINGERPRINT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap index fe61840bcc6..a754ef93e28 100644 --- a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap +++ b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap @@ -2,15 +2,23 @@ "versions": { "content": [ [ - "versions.yml:md5,90dca36c10677c9d6ad5ef7e42c4d788" + "versions.yml:md5,cbf898a998bb9b90d2e4110ee343d674" ] ], - "timestamp": "2023-12-04T15:53:39.112154" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T09:53:08.359314244" }, "extract_fingerprint": { "content": [ "##fileformat=VCFv4.2" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2023-12-04T15:53:39.12594" } } \ No newline at end of file diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml index 1912c391791..4c97b78f329 100644 --- a/modules/nf-core/picard/fastqtosam/environment.yml +++ b/modules/nf-core/picard/fastqtosam/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index eac5b947f9d..dedd70a0318 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -4,8 +4,8 @@ process PICARD_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml index 3fe7207ce64..88248ad425e 100644 --- a/modules/nf-core/picard/filtersamreads/environment.yml +++ b/modules/nf-core/picard/filtersamreads/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index f64e4a05d63..32977bdc306 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -4,8 +4,8 @@ process PICARD_FILTERSAMREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml index 890c13a2aa9..cf197ce646f 100644 --- a/modules/nf-core/picard/fixmateinformation/environment.yml +++ b/modules/nf-core/picard/fixmateinformation/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index 85519558a6c..bf29e24cc07 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -4,8 +4,8 @@ process PICARD_FIXMATEINFORMATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index e953ec958cf..16dd9f61307 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index ab7212a101a..e47b74f787e 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f54a8..a27db11865c 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index ad0b296361b..cf18ac35ca9 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index eb17111e4c5..24a57d0e3e0 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "sorted_bam_versions": { "content": [ [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-20T15:31:50.928021" + "timestamp": "2024-07-10T09:49:13.838237323" }, "unsorted_bam_name": { "content": [ @@ -25,29 +25,29 @@ "content": [ [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-20T15:25:47.518152" + "timestamp": "2024-07-10T09:49:32.685023439" }, "sorted_bam_metrics": { "content": [ [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-21T11:39:10.318331" + "timestamp": "2024-07-10T09:49:13.788936246" }, "cram_name": { "content": [ @@ -62,40 +62,40 @@ "cram_versions": { "content": [ [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-01-19T10:27:03.26989" + "timestamp": "2024-07-10T09:49:32.731312566" }, "unsorted_bam_versions": { "content": [ [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-20T15:31:24.040403" + "timestamp": "2024-07-10T09:48:57.466503381" }, "unsorted_bam_metrics": { "content": [ [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-21T10:51:12.831787" + "timestamp": "2024-07-10T09:48:57.387579606" }, "sorted_bam_name": { "content": [ diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml index c3bffb0c070..af6a04a1613 100644 --- a/modules/nf-core/picard/mergesamfiles/environment.yml +++ b/modules/nf-core/picard/mergesamfiles/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 8044ab207b8..1e6e2274b9f 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -4,8 +4,8 @@ process PICARD_MERGESAMFILES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index 3e7d8eb5a64..b7ccb0089f3 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index d44b1829c48..3e4f38caa3c 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,8 +5,8 @@ process PICARD_RENAMESAMPLEINVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml index 9adb3b2529a..b36f96bf1ce 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf index ebd2a66bcae..344284804a1 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/main.nf +++ b/modules/nf-core/picard/scatterintervalsbyns/main.nf @@ -4,8 +4,8 @@ process PICARD_SCATTERINTERVALSBYNS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml index 5fee08c1480..967b9f9f567 100644 --- a/modules/nf-core/picard/sortsam/environment.yml +++ b/modules/nf-core/picard/sortsam/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index 513a23f32d0..af23e294bed 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index f1dbb6b9317..a2f96e80fd3 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 5359caae38a..7133c13ae0c 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : + 'biocontainers/picard:3.2.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index e2e4a947cfa..8ff332c8b4a 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,15 +2,15 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", + "test.cram.crai:md5,cb5268070f99cdd0d86f43613e5fc7db", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", "test.stats:md5,372a7d9d9081aa009b21343a913beb14", [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ] ], @@ -18,7 +18,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-03T11:55:09.400487" + "timestamp": "2024-07-10T09:50:25.483402093" }, "sarscov2 - bam - stub": { "content": [ @@ -101,8 +101,8 @@ "9": [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ], "bai": [ @@ -183,8 +183,8 @@ "versions": [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ] } @@ -193,7 +193,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-03T11:55:22.514635" + "timestamp": "2024-07-10T09:50:45.745539171" }, "homo_sapiens - cram - stub": { "content": [ @@ -268,8 +268,8 @@ "9": [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ], "bai": [ @@ -342,8 +342,8 @@ "versions": [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ] } @@ -352,20 +352,20 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-03T11:55:37.258086" + "timestamp": "2024-07-10T09:51:17.13987629" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", - "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", + "test.bam:md5,d1a53820e4a6e42ca8aceab51d74cf57", + "test.bam.bai:md5,be9485a644813773fb893a0a6b9b977c", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574", [ "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", "versions.yml:md5,fcf804c605f455127f2449403d70390c" ] ], @@ -373,6 +373,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.2" }, - "timestamp": "2024-07-03T11:54:53.226702" + "timestamp": "2024-07-10T09:50:01.597322113" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap index 4e80c28cab4..f02de25e29c 100644 --- a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap @@ -57,15 +57,15 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,d04aca83a6423efc7b818b0d3e0cb1ba", - "versions.yml:md5,e0ec5ed2685f50270d45602c891fad3b" + "versions.yml:md5,d61a29a9b3d8c60ed90b068df8032979", + "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-06-07T10:41:38.304686" + "timestamp": "2024-07-10T09:38:29.298437201" }, "sascov2_wgs - [bam,bai]": { "content": [ @@ -114,14 +114,14 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,600deaee68c6f78bbdf023b794d7b4fe", - "versions.yml:md5,d04aca83a6423efc7b818b0d3e0cb1ba" + "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d", + "versions.yml:md5,ebe92bff64a6e7b1a0aa741674d24893" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2023-11-29T17:32:57.186833877" + "timestamp": "2024-07-10T09:38:09.338919835" } } \ No newline at end of file