Merge pull request #164 from drpatelh/fixes

Add missing build ids and rename *.txt channels

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 {

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 {

software/bcftools/stats/main.nf

@@ -21,7 +21,7 @@ process BCFTOOLS_STATS {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.txt"), emit: stats
+    tuple val(meta), path("*stats.txt"), emit: stats
     path  "*.version.txt"              , emit: version
 
     script:

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

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 {

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 {

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

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 {