From a23a013dcc2a5d6e66eb8ab403bf1928887a2adb Mon Sep 17 00:00:00 2001 From: asp8200 Date: Mon, 29 Apr 2024 14:34:32 +0000 Subject: [PATCH 1/5] Update mosdepth --- modules.json | 2 +- modules/nf-core/mosdepth/environment.yml | 2 +- modules/nf-core/mosdepth/main.nf | 4 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 120 +++++++++--------- 4 files changed, 64 insertions(+), 64 deletions(-) diff --git a/modules.json b/modules.json index 747c53a5f5..dda7cb585b 100644 --- a/modules.json +++ b/modules.json @@ -316,7 +316,7 @@ }, "mosdepth": { "branch": "master", - "git_sha": "30d3ca4346ae38f0de821c57a9c517b8b0b135d6", + "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", "installed_by": ["modules"] }, "msisensorpro/msisomatic": { diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index 88c7126c05..bcb9d64a7a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.6 + - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 0190a09d80..6f4a838343 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index 00f4cd974b..c604540b03 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -222,15 +222,15 @@ ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:29:04.084192" + "timestamp": "2024-04-29T13:33:16.953408231" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -260,7 +260,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -289,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -367,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -395,15 +395,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:16.664319" + "timestamp": "2024-04-29T13:32:50.160217828" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -433,7 +433,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -456,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -480,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "global_txt": [ @@ -507,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -528,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "regions_bed": [ @@ -556,15 +556,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:35.978752" + "timestamp": "2024-04-29T13:33:01.164885111" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -594,7 +594,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -623,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -641,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -674,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -701,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -729,15 +729,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:27:55.598384" + "timestamp": "2024-04-29T13:32:39.071657456" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -767,7 +767,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -775,7 +775,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "3": [ @@ -796,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -814,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "8": [ @@ -847,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -874,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "regions_txt": [ @@ -883,7 +883,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "summary_txt": [ @@ -902,15 +902,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:26.37386" + "timestamp": "2024-04-29T13:32:55.631776118" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -940,7 +940,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -963,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1002,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1039,15 +1039,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:27:44.658599" + "timestamp": "2024-04-29T13:32:33.642125299" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -1077,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -1100,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1139,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1176,15 +1176,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:06.482838" + "timestamp": "2024-04-29T13:32:44.704920941" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -1222,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -1255,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1273,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -1306,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1333,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -1369,18 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-03-28T12:28:45.918241" + "timestamp": "2024-04-29T13:33:06.737266831" } } \ No newline at end of file From da76e252ac2469e0f88dd7d36efbeedb45e4caf3 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 06:16:03 +0000 Subject: [PATCH 2/5] Updating md5sums in tests --- tests/test_markduplicates_from_bam.yml | 12 ++++++------ tests/test_markduplicates_from_cram.yml | 12 ++++++------ tests/test_save_mapped.yml | 8 ++++---- tests/test_save_output_as_bam_only.yml | 8 ++++---- tests/test_tumor_normal_pair.yml | 16 ++++++++-------- 5 files changed, 28 insertions(+), 28 deletions(-) diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml index d6191216bd..dee1fd68c1 100644 --- a/tests/test_markduplicates_from_bam.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -73,23 +73,23 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml index f36619f719..0123826c68 100644 --- a/tests/test_markduplicates_from_cram.yml +++ b/tests/test_markduplicates_from_cram.yml @@ -70,23 +70,23 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 + md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 + md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml index 7868da9d35..a4b10fead3 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_save_mapped.yml @@ -40,9 +40,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -50,9 +50,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml index bc577c0ae8..bd8b19f803 100644 --- a/tests/test_save_output_as_bam_only.yml +++ b/tests/test_save_output_as_bam_only.yml @@ -34,9 +34,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -44,9 +44,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml index b616fc2b83..0be73ea719 100644 --- a/tests/test_tumor_normal_pair.yml +++ b/tests/test_tumor_normal_pair.yml @@ -45,9 +45,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b + md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -55,9 +55,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b + md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt @@ -65,9 +65,9 @@ - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 + md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt @@ -75,9 +75,9 @@ - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 + md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats From b8ba32efbf43e632065574763d3cfffcf8176689 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 06:32:51 +0000 Subject: [PATCH 3/5] Updating md5sums in tests --- tests/test_default.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/test_default.yml b/tests/test_default.yml index 5368cfd9b0..84f14e05f2 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -36,9 +36,9 @@ - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt @@ -46,9 +46,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 + md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 + md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats From 3aabdd871946df015f5e1cc3bcc5ff0b211f283c Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 07:32:59 +0000 Subject: [PATCH 4/5] Updating md5sums in tests --- tests/test_skip_markduplicates.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index d683b6952d..a39adefd96 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -28,9 +28,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -38,9 +38,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -84,9 +84,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -94,9 +94,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -138,9 +138,9 @@ - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt @@ -148,9 +148,9 @@ - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 67ac075b077723fb1cce4b026dcdf0af + md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3230b6808c22d4907d18910f2dc2daf2 + md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats From 68404a8199b07c3bc51710efa0abda4113d632a9 Mon Sep 17 00:00:00 2001 From: asp8200 Date: Tue, 30 Apr 2024 07:57:02 +0000 Subject: [PATCH 5/5] Update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f4236d42a7..f0c59ee268 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1482](https://github.com/nf-core/sarek/pull/1482) - Pin `nf-prov` plugin to `1.2.2` - [#1485](https://github.com/nf-core/sarek/pull/1485) - Update citation for publication - [#1487](https://github.com/nf-core/sarek/pull/1487) - Update sentieon-modules to Sentieon `202308.02` +- [#1490](https://github.com/nf-core/sarek/pull/1490) - Update mosdepth to `0.3.8` ### Fixed @@ -27,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | +| `mosdepth` | 0.3.6 | 0.3.8 | | `sentieon` | 202308.01 | 202308.02 | ### Modules / Subworkflows