Merge pull request #806 from drpatelh/updates

Replace vanilla Linux Biocontainer in all modules with Ubuntu

Author: drpatelh

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - [[#791](https://github.com/nf-core/rnaseq/issues/791)] - Add outputs for umitools dedup summary stats
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 

modules.json

@@ -7,7 +7,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "cat/fastq": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
             },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -22,7 +22,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gunzip": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
             },
             "hisat2/align": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -118,7 +118,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "untar": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
             }
         }
     }

modules/local/rsem_merge_counts.nf

@@ -3,8 +3,8 @@ process RSEM_MERGE_COUNTS {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     path ('genes/*')

modules/nf-core/modules/cat/fastq/main.nf

@@ -133,7 +133,7 @@ workflow PREPARE_GENOME {
     if ('bbsplit' in prepare_tool_indices) {
         if (params.bbsplit_index) {
             if (params.bbsplit_index.endsWith('.tar.gz')) {
-                ch_bbsplit_index = UNTAR_BBSPLIT_INDEX ( params.bbsplit_index ).untar
+                ch_bbsplit_index = UNTAR_BBSPLIT_INDEX ( [ [:], params.bbsplit_index ] ).untar.map { it[1] }
                 ch_versions      = ch_versions.mix(UNTAR_BBSPLIT_INDEX.out.versions)
             } else {
                 ch_bbsplit_index = file(params.bbsplit_index)
@@ -160,7 +160,7 @@ workflow PREPARE_GENOME {
     if ('star_salmon' in prepare_tool_indices) {
         if (params.star_index) {
             if (params.star_index.endsWith('.tar.gz')) {
-                ch_star_index = UNTAR_STAR_INDEX ( params.star_index ).untar
+                ch_star_index = UNTAR_STAR_INDEX ( [ [:], params.star_index ] ).untar.map { it[1] }
                 ch_versions   = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
             } else {
                 ch_star_index = file(params.star_index)
@@ -178,7 +178,7 @@ workflow PREPARE_GENOME {
     if ('star_rsem' in prepare_tool_indices) {
         if (params.rsem_index) {
             if (params.rsem_index.endsWith('.tar.gz')) {
-                ch_rsem_index = UNTAR_RSEM_INDEX ( params.rsem_index ).untar
+                ch_rsem_index = UNTAR_RSEM_INDEX ( [ [:], params.rsem_index ] ).untar.map { it[1] }
                 ch_versions   = ch_versions.mix(UNTAR_RSEM_INDEX.out.versions)
             } else {
                 ch_rsem_index = file(params.rsem_index)
@@ -203,7 +203,7 @@ workflow PREPARE_GENOME {
         }
         if (params.hisat2_index) {
             if (params.hisat2_index.endsWith('.tar.gz')) {
-                ch_hisat2_index = UNTAR_HISAT2_INDEX ( params.hisat2_index ).untar
+                ch_hisat2_index = UNTAR_HISAT2_INDEX ( [ [:], params.hisat2_index ] ).untar.map { it[1] }
                 ch_versions     = ch_versions.mix(UNTAR_HISAT2_INDEX.out.versions)
             } else {
                 ch_hisat2_index = file(params.hisat2_index)
@@ -221,7 +221,7 @@ workflow PREPARE_GENOME {
     if ('salmon' in prepare_tool_indices) {
         if (params.salmon_index) {
             if (params.salmon_index.endsWith('.tar.gz')) {
-                ch_salmon_index = UNTAR_SALMON_INDEX ( params.salmon_index ).untar
+                ch_salmon_index = UNTAR_SALMON_INDEX ( [ [:], params.salmon_index ] ).untar.map { it[1] }
                 ch_versions     = ch_versions.mix(UNTAR_SALMON_INDEX.out.versions)
             } else {
                 ch_salmon_index = file(params.salmon_index)