From 0b33b6d0817513935b58e36a0d38f5510b508cf3 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Tue, 9 Feb 2021 23:03:13 +0000 Subject: [PATCH 1/5] Add missing build ids --- software/bandage/image/main.nf | 2 +- software/bcftools/consensus/main.nf | 2 +- software/bedtools/maskfasta/main.nf | 2 +- software/gunzip/main.nf | 2 +- software/untar/main.nf | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/software/bandage/image/main.nf b/software/bandage/image/main.nf index 7f311746..57b5f23f 100644 --- a/software/bandage/image/main.nf +++ b/software/bandage/image/main.nf @@ -11,7 +11,7 @@ process BANDAGE_IMAGE { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? 'bioconda::bandage=0.8.1' : null) + conda (params.enable_conda ? 'bioconda::bandage=0.8.1=hc9558a2_2' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/bandage:0.8.1--hc9558a2_2" } else { diff --git a/software/bcftools/consensus/main.nf b/software/bcftools/consensus/main.nf index c74d21d0..1e640542 100644 --- a/software/bcftools/consensus/main.nf +++ b/software/bcftools/consensus/main.nf @@ -10,7 +10,7 @@ process BCFTOOLS_CONSENSUS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::bcftools=1.11" : null) + conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0" } else { diff --git a/software/bedtools/maskfasta/main.nf b/software/bedtools/maskfasta/main.nf index ccd93df7..1051a80e 100644 --- a/software/bedtools/maskfasta/main.nf +++ b/software/bedtools/maskfasta/main.nf @@ -11,7 +11,7 @@ process BEDTOOLS_MASKFASTA { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) + conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0" } else { diff --git a/software/gunzip/main.nf b/software/gunzip/main.nf index 20f6467d..b9647a4a 100644 --- a/software/gunzip/main.nf +++ b/software/gunzip/main.nf @@ -10,7 +10,7 @@ process GUNZIP { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } - conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img" } else { diff --git a/software/untar/main.nf b/software/untar/main.nf index 8912fb0b..62596ef6 100644 --- a/software/untar/main.nf +++ b/software/untar/main.nf @@ -10,7 +10,7 @@ process UNTAR { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } - conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img" } else { From d50d070c064a7d4913bd92bdc3772acb85700050 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Tue, 9 Feb 2021 23:09:18 +0000 Subject: [PATCH 2/5] Change txt channel output --- software/bcftools/stats/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/software/bcftools/stats/main.nf b/software/bcftools/stats/main.nf index f0b81457..ffb9a468 100644 --- a/software/bcftools/stats/main.nf +++ b/software/bcftools/stats/main.nf @@ -21,8 +21,8 @@ process BCFTOOLS_STATS { tuple val(meta), path(vcf) output: - tuple val(meta), path("*.txt"), emit: stats - path "*.version.txt" , emit: version + tuple val(meta), path("*stats.txt"), emit: stats + path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) From 2b9129b3f9be9383280ad7621dafaeafde932ba9 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Tue, 9 Feb 2021 23:09:22 +0000 Subject: [PATCH 3/5] Change txt channel output --- software/stringtie/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/software/stringtie/main.nf b/software/stringtie/main.nf index e624354b..1d69bb50 100644 --- a/software/stringtie/main.nf +++ b/software/stringtie/main.nf @@ -25,7 +25,7 @@ process STRINGTIE { output: tuple val(meta), path("*.coverage.gtf") , emit: coverage_gtf tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf - tuple val(meta), path("*.txt") , emit: abundance + tuple val(meta), path("*.abundance.txt") , emit: abundance tuple val(meta), path("*.ballgown") , emit: ballgown path "*.version.txt" , emit: version @@ -45,7 +45,7 @@ process STRINGTIE { $strandedness \\ -G $gtf \\ -o ${prefix}.transcripts.gtf \\ - -A ${prefix}.gene_abundance.txt \\ + -A ${prefix}.gene.abundance.txt \\ -C ${prefix}.coverage.gtf \\ -b ${prefix}.ballgown \\ $options.args From d2508e3c0308ff601aa30b5f21d3a2e1eac85d75 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 10 Feb 2021 12:51:47 +0000 Subject: [PATCH 4/5] Amend prefix for bcftools stats --- software/bcftools/stats/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/bcftools/stats/meta.yml b/software/bcftools/stats/meta.yml index fd8319e6..24ee2e36 100644 --- a/software/bcftools/stats/meta.yml +++ b/software/bcftools/stats/meta.yml @@ -52,7 +52,7 @@ output: - stats: type: file description: Text output file containing stats - pattern: "*.{txt}" + pattern: "*.{stats.txt}" - version: type: file description: File containing software version From b9afca2b057f431a59bf05afa525b165cc309e0c Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 10 Feb 2021 12:53:17 +0000 Subject: [PATCH 5/5] Underscore not . --- software/bcftools/stats/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/software/bcftools/stats/meta.yml b/software/bcftools/stats/meta.yml index 24ee2e36..75ed50f4 100644 --- a/software/bcftools/stats/meta.yml +++ b/software/bcftools/stats/meta.yml @@ -52,7 +52,7 @@ output: - stats: type: file description: Text output file containing stats - pattern: "*.{stats.txt}" + pattern: "*_{stats.txt}" - version: type: file description: File containing software version