Merge branch 'dev' into remove_tags.yml

Author: drpatelh

.github/workflows/ci.yml

@@ -256,7 +256,7 @@ jobs:
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ !contains(needs.*.result, 'failure') }}
+        if: ${{ success() }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

CHANGELOG.md

@@ -12,15 +12,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Properly update qualimap/rnaseq module (ie not patch)
 - [PR #1201](https://github.com/nf-core/rnaseq/pull/1201) - Template update for nf-core/tools v2.12
 - [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config`
-- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
 - [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules
-- [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831))
+- [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions
 - [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats
+- [PR #1214](https://github.com/nf-core/rnaseq/pull/1214) - Bump umitools + delocalise prepareforrsem ([#831](https://github.com/nf-core/rnaseq/issues/831))
 - [PR #1216](https://github.com/nf-core/rnaseq/pull/1216) - Delocalise catadditionalfasta ([#1162](https://github.com/nf-core/rnaseq/issues/1162))
 - [PR #1218](https://github.com/nf-core/rnaseq/pull/1218) - Template update for nf-core/tools v2.13
 - [PR #1220](https://github.com/nf-core/rnaseq/pull/1220) - Initialise nf-test and add pipeline level test
 - [PR #1221](https://github.com/nf-core/rnaseq/pull/1221) - Use nf-test test for all nf-core components
 - [PR #1226](https://github.com/nf-core/rnaseq/pull/1226) - Reuse bbsplit index and don't keep overwriting ([#1225](https://github.com/nf-core/rnaseq/issues/1225))
+- [PR #1228](https://github.com/nf-core/rnaseq/pull/1228) - Make README usage consistent with docs/usage.md
 - [PR #1229](https://github.com/nf-core/rnaseq/pull/1229) - Template update for nf-core/tools v2.13.1
 - [PR #1231](https://github.com/nf-core/rnaseq/pull/1231) - Add sortmerna index possibilities
 - [PR #1232](https://github.com/nf-core/rnaseq/pull/1232) - Add nf-test tests to star_genomegenerate_igenomes
@@ -35,7 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1241](https://github.com/nf-core/rnaseq/pull/1241) - Add nf-test tests to deseq2_qc
 - [PR #1242](https://github.com/nf-core/rnaseq/pull/1242) - Use dupradar from nf-core/modules
 - [PR #1244](https://github.com/nf-core/rnaseq/pull/1244) - Add gtf2bed tests
-- [PR #1250](https://github.com/nf-core/rnaseq/pull/1244) - Remove all tags.yml files because the testing system has changed
+- [PR #1250](https://github.com/nf-core/rnaseq/pull/1250) - Remove all tags.yml files because the testing system has changed
 
 ### Parameters
 

README.md

@@ -80,9 +80,10 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/rnaseq \
-    --input samplesheet.csv \
+    --input <SAMPLESHEET> \
     --outdir <OUTDIR> \
-    --genome GRCh37 \
+    --gtf <GTF> \
+    --fasta <GENOME FASTA> \
     -profile <docker/singularity/.../institute>
 ```
 

docs/usage.md

@@ -213,8 +213,6 @@ nextflow run \
     --outdir <OUTDIR> \
     --gtf <GTF> \
     --fasta <GENOME FASTA> \
-    --igenomes_ignore \
-    --genome null \
     -profile docker
 ```
 

modules/local/deseq2_qc/tests/data/countFile.tsv

@@ -9,10 +9,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file("${moduleTestDir}/data/countFile.tsv")
-                input[1] = file("${moduleTestDir}/data/deseq2_pca_header.txt")
-                input[2] = file("${moduleTestDir}/data/deseq2_clustering_header.txt")
-                """.stripIndent().trim()
+                input[0] = file(params.pipelines_testdata_base_path + "deseq2qc/countFile.tsv", checkIfExists: true)
+                input[1] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_pca_header.txt", checkIfExists: true)
+                input[2] = file(params.pipelines_testdata_base_path + "deseq2qc/deseq2_clustering_header.txt", checkIfExists: true)
+                """
             }
         }