Merge pull request #93 from nf-core/fix-publishing

fix: use parameter for publishing mode
nf-core · May 17, 2022 · 922e81c · 922e81c
2 parents 1751937 + e697f22
commit 922e81c
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Showing 2 changed files with 17 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#57](https://github.com/nf-core/fetchngs/pull/57) - fetchngs fails if FTP is blocked
 - [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
+- [#93](https://github.com/nf-core/fetchngs/pull/93) - Adjust modules configuration to respect the `publish_dir_mode` parameter.
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -24,7 +24,7 @@ process {
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*_versions.yml'
         ]
     }
@@ -48,7 +48,7 @@ if (params.input_type == 'sra') {
         withName: SRA_RUNINFO_TO_FTP {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -58,12 +58,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -80,12 +80,12 @@ if (params.input_type == 'sra') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -101,15 +101,15 @@ if (params.input_type == 'sra') {
         withName: SRA_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
 
         withName: MULTIQC_MAPPINGS_CONFIG {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -129,7 +129,7 @@ if (params.input_type == 'synapse') {
             ext.args = '--long'
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -138,12 +138,12 @@ if (params.input_type == 'synapse') {
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },
-                    mode: 'copy',
-                    pattern: "*gz"
+                    mode: params.publish_dir_mode,
+                    pattern: "*.fastq.gz"
                 ],
                 [
                     path: { "${params.outdir}/fastq/md5" },
-                    mode: 'copy',
+                    mode: params.publish_dir_mode,
                     pattern: "*.md5"
                 ]
             ]
@@ -152,7 +152,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_SHOW {
             publishDir = [
                 path: { "${params.outdir}/metadata" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
@@ -167,7 +167,7 @@ if (params.input_type == 'synapse') {
         withName: SYNAPSE_MERGE_SAMPLESHEET {
             publishDir = [
                 path: { "${params.outdir}/samplesheet" },
-                mode: 'copy',
+                mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }