Improve reproducibility with Conda

.github/workflows/nf-test.yml

@@ -59,7 +59,7 @@ jobs:
         env:
           NFT_VER: ${{ env.NFT_VER }}
         with:
-          max_shards: 7
+          max_shards: 14
 
       - name: debug
         run: |

CHANGELOG.md

@@ -38,6 +38,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1558](https://github.com/nf-core/rnaseq/pull/1558) - Remove patches and bump modules for ARM compat
 - [PR #1560](https://github.com/nf-core/rnaseq/pull/1560) - General modules update, include updating subworkflows for stats fixes
 - [PR #1563](https://github.com/nf-core/rnaseq/pull/1563) - Version bumps ahead of 3.19.0 release
+- [PR #1565](https://github.com/nf-core/rnaseq/pull/1565) - Improve reproducibility with Conda
 
 # 3.18.0 - 2024-12-19
 

modules.json

@@ -275,17 +275,20 @@
                     "umitools/dedup": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["bam_dedup_stats_samtools_umitools"]
+                        "installed_by": ["bam_dedup_stats_samtools_umitools", "modules"],
+                        "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff"
                     },
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore", "modules"],
+                        "patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
                     },
                     "umitools/prepareforrsem": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["bam_dedup_umi", "modules"]
+                        "installed_by": ["bam_dedup_umi", "modules"],
+                        "patch": "modules/nf-core/umitools/prepareforrsem/umitools-prepareforrsem.diff"
                     },
                     "untar": {
                         "branch": "master",

modules/local/deseq2_qc/environment.yml

@@ -2,12 +2,12 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::r-base
-  - conda-forge::r-optparse
-  - conda-forge::r-ggplot2
-  - conda-forge::r-rcolorbrewer
-  - conda-forge::r-pheatmap
-  - bioconda::bioconductor-deseq2
-  - bioconda::bioconductor-biocparallel
-  - bioconda::bioconductor-tximport
-  - bioconda::bioconductor-complexheatmap
+  - conda-forge::r-base=4.0.3
+  - conda-forge::r-optparse=1.6.6
+  - conda-forge::r-ggplot2=3.3.2
+  - conda-forge::r-rcolorbrewer=1.1.2
+  - conda-forge::r-pheatmap=1.0.12
+  - bioconda::bioconductor-deseq2=1.28.0
+  - bioconda::bioconductor-biocparallel=1.22.0
+  - bioconda::bioconductor-tximport=1.16.0
+  - bioconda::bioconductor-complexheatmap=2.4.2

modules/local/deseq2_qc/tests/main.nf.test

@@ -22,11 +22,8 @@ nextflow_process {
                 { assert snapshot(
                     process.out.dists_multiqc,
                     process.out.dists_txt,
-                    process.out.log,
                     process.out.pca_multiqc,
                     process.out.pca_txt,
-                    process.out.rdata,
-                    process.out.size_factors,
                     process.out.versions
                 ).match() }
             )

modules/local/deseq2_qc/tests/main.nf.test.snap

@@ -12,13 +12,13 @@
                     "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "3": [
-
+                    
                 ],
                 "4": [
                     "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "5": [
-
+                    
                 ],
                 "6": [
                     "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -37,7 +37,7 @@
                     "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
                 ],
                 "dists_multiqc": [
-
+                    
                 ],
                 "dists_txt": [
                     "deseq2.sample.dists.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -46,7 +46,7 @@
                     "R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "pca_multiqc": [
-
+                    
                 ],
                 "pca_txt": [
                     "deseq2.pca.vals.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -81,41 +81,25 @@
     "parse count data correctly": {
         "content": [
             [
-
+                
             ],
             [
                 "deseq2.sample.dists.txt:md5,1616ce40eb58ee75640efed219c6bbec"
             ],
             [
-                "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676"
-            ],
-            [
-
+
             ],
             [
                 "deseq2.pca.vals.txt:md5,4cda8e32ec39326c1350e77b4b607aad"
             ],
-            [
-                "deseq2.dds.RData:md5,c7c1872e7566321d0c3f7ca56c463088"
-            ],
-            [
-                [
-                    "RAP1_IAA_30M_REP1.txt:md5,ce4ff0b74aeedc3dc12a764c3504c9df",
-                    "RAP1_UNINDUCED_REP1.txt:md5,51c9b23be5e82670aceb14f7e58dd867",
-                    "RAP1_UNINDUCED_REP2.txt:md5,2c56106abcd9d31980f672b6e2862ee8",
-                    "WT_REP1.txt:md5,5e3fe5f7e9b7f300be43649a8b496352",
-                    "WT_REP2.txt:md5,2ce093f2c2e92c1bde1cd3da91ac884c",
-                    "deseq2.size_factors.RData:md5,51c6643a0f8a9edabbff8df0165451f2"
-                ]
-            ],
             [
                 "versions.yml:md5,60f8e4f473397a4b5d1a3dc490c93ec5"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2024-06-21T11:21:20.349616"
+        "timestamp": "2025-06-06T11:39:25.276180757"
     }
-}
+}

modules/local/gtf2bed/environment.yml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::perl>=5.26.2
+  - conda-forge::perl=5.26.2

subworkflows/local/align_star/tests/main.nf.test

@@ -63,16 +63,14 @@ nextflow_workflow {
                 { assert snapshot(
                     file(workflow.out.log_final[0][1]).name,
                     file(workflow.out.log_out[0][1]).name,
-                    workflow.out.bai,
-                    workflow.out.bam,
-                    workflow.out.bam_sorted,
-                    workflow.out.bam_transcript,
+                    file(workflow.out.bai[0][1]).name,
+                    bam(workflow.out.bam[0][1]).getReadsMD5(),
                     workflow.out.csi,
                     workflow.out.log_progress,
                     workflow.out.fastq,
                     workflow.out.flagstat,
                     workflow.out.idxstats,
-                    workflow.out.orig_bam,
+                    bam(workflow.out.orig_bam[0][1]).getReadsMD5(),
                     workflow.out.stats,
                     workflow.out.tab,
                     workflow.out.versions).match()}
@@ -132,16 +130,14 @@ nextflow_workflow {
                 { assert snapshot(
                     file(workflow.out.log_final[0][1]).name,
                     file(workflow.out.log_out[0][1]).name,
-                    workflow.out.bai,
-                    workflow.out.bam,
-                    workflow.out.bam_sorted,
-                    workflow.out.bam_transcript,
+                    file(workflow.out.bai[0][1]).name,
+                    bam(workflow.out.bam[0][1]).getReadsMD5(),
                     workflow.out.csi,
                     workflow.out.log_progress,
                     workflow.out.fastq,
                     workflow.out.flagstat,
                     workflow.out.idxstats,
-                    workflow.out.orig_bam,
+                    bam(workflow.out.orig_bam[0][1]).getReadsMD5(),
                     workflow.out.stats,
                     workflow.out.tab,
                     workflow.out.versions).match()}