From 208415c5f7aa7e620004904a714af02efed724f4 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 14 Apr 2023 10:56:18 +0200 Subject: [PATCH 1/4] Bump chromap/index version --- modules/nf-core/chromap/index/main.nf | 6 +++--- tests/modules/nf-core/chromap/index/test.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf index 0630c614d35..25ee6a7eb63 100644 --- a/modules/nf-core/chromap/index/main.nf +++ b/modules/nf-core/chromap/index/main.nf @@ -2,10 +2,10 @@ process CHROMAP_INDEX { tag "$fasta" label 'process_medium' - conda "bioconda::chromap=0.2.1" + conda "bioconda::chromap=0.2.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : - 'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }" + 'https://depot.galaxyproject.org/singularity/chromap:0.2.4--hd03093a_0' : + 'quay.io/biocontainers/chromap:0.2.4--hd03093a_0' }" input: tuple val(meta), path(fasta) diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml index d71767471d8..b5e6f74f92d 100644 --- a/tests/modules/nf-core/chromap/index/test.yml +++ b/tests/modules/nf-core/chromap/index/test.yml @@ -5,5 +5,5 @@ - chromap files: - path: output/chromap/genome.index + md5sum: 4f30e1b5c7cb8575e24842c75d43a3dd - path: output/chromap/versions.yml - md5sum: fc5c80190d0622ea3e979e6862f8e32b From cacf679c45de47bb13734cbfbad1a43857a92ee7 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 14 Apr 2023 10:56:40 +0200 Subject: [PATCH 2/4] Bump chromap/chromap version --- modules/nf-core/chromap/chromap/main.nf | 6 +++--- tests/modules/nf-core/chromap/chromap/test.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf index f47995b3756..5b7631cb54c 100644 --- a/modules/nf-core/chromap/chromap/main.nf +++ b/modules/nf-core/chromap/chromap/main.nf @@ -2,10 +2,10 @@ process CHROMAP_CHROMAP { tag "$meta.id" label 'process_medium' - conda "bioconda::chromap=0.2.1 bioconda::samtools=1.16.1" + conda "bioconda::chromap=0.2.4 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' : - 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' : + 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' }" input: tuple val(meta), path(reads) diff --git a/tests/modules/nf-core/chromap/chromap/test.yml b/tests/modules/nf-core/chromap/chromap/test.yml index 6c507773387..7c1a9a0edcf 100644 --- a/tests/modules/nf-core/chromap/chromap/test.yml +++ b/tests/modules/nf-core/chromap/chromap/test.yml @@ -28,5 +28,5 @@ files: - path: output/chromap/genome.index - path: output/chromap/test.bam - md5sum: 28ccaa8e39ecf5617dc270bdd7ddf1ba + md5sum: 7f8af20a3fa52b2a8967977f0376f466 - path: output/chromap/versions.yml From 310c1aa66cae757b8afb67757d47bd0ea4da10ec Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 14 Apr 2023 10:56:53 +0200 Subject: [PATCH 3/4] Update md5 hash --- tests/subworkflows/nf-core/fastq_align_chromap/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml index c9b49f7bb16..0e79cd7d4f7 100644 --- a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml +++ b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml @@ -51,7 +51,7 @@ - path: ./output/samtools/test.sorted.bam.bai # samtools stats - path: ./output/samtools/test.sorted.bam.flagstat - md5sum: 7845b46e1dfdb6cea776bab7acf6f1e3 + md5sum: 2fa0d90162a1b655863796c2a6bd8f45 - path: ./output/samtools/test.sorted.bam.idxstats md5sum: 1adb27b52d4d64b826f48b59d61dcd4d - path: ./output/samtools/test.sorted.bam.stats From b0e0de945df69ce44b550d8cd06e6cc760cec3a6 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 14 Apr 2023 11:15:36 +0200 Subject: [PATCH 4/4] Fix conda test --- tests/modules/nf-core/chromap/index/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml index b5e6f74f92d..e3de1391482 100644 --- a/tests/modules/nf-core/chromap/index/test.yml +++ b/tests/modules/nf-core/chromap/index/test.yml @@ -5,5 +5,4 @@ - chromap files: - path: output/chromap/genome.index - md5sum: 4f30e1b5c7cb8575e24842c75d43a3dd - path: output/chromap/versions.yml