Merge pull request #1240 from maxulysse/fix_params

Fix genomes params usage
nf-core · Mar 7, 2024 · 8914c35 · 8914c35
2 parents 704212b + 7412996
commit 8914c35
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Showing 3 changed files with 15 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,11 +19,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [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 #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 #1234](https://github.com/nf-core/rnaseq/pull/1234) - Switch to genomecov from nf-core
-- [PR #1242](https://github.com/nf-core/rnaseq/pull/1234) - Switch to dupradar from nf-core
+- [PR #1232](https://github.com/nf-core/rnaseq/pull/1232) - Add nf-test tests to star_genomegenerate_igenomes
+- [PR #1233](https://github.com/nf-core/rnaseq/pull/1233) - Add nf-test tests to star_align_igenomes
+- [PR #1234](https://github.com/nf-core/rnaseq/pull/1234) - Use genomecov from nf-core/modules
+- [PR #1235](https://github.com/nf-core/rnaseq/pull/1235) - Add nf-test tests to gtf_filter
+- [PR #1236](https://github.com/nf-core/rnaseq/pull/1236) - Add nf-test tests to utils_nfcore_rnaseq_pipeline
+- [PR #1237](https://github.com/nf-core/rnaseq/pull/1237) - Fix concurrency error in Github CI workflow
+- [PR #1238](https://github.com/nf-core/rnaseq/pull/1238) - Add nf-test tests to preprocess_transcripts_fasta_gencode
+- [PR #1239](https://github.com/nf-core/rnaseq/pull/1239) - Add nf-test tests to align_star
+- [PR #1240](https://github.com/nf-core/rnaseq/pull/1240) - Fix reference files params usage
+- [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
 
 ### Parameters
 

diff --git a/nextflow.config b/nextflow.config
@@ -12,20 +12,6 @@ params {
     // Input options
     input                      = null
 
-    // References files
-    additional_fasta           = null
-    bbsplit_index              = null
-    fasta                      = null
-    gene_bed                   = null
-    gff                        = null
-    gtf                        = null
-    hisat2_index               = null
-    kallisto_index             = null
-    rsem_index                 = null
-    salmon_index               = null
-    star_index                 = null
-    transcript_fasta           = null
-
     // References
     genome                     = null
     splicesites                = null
@@ -143,7 +129,7 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
+    validationSchemaIgnoreParams     = 'genomes,igenomes_base,additional_fasta,bbsplit_index,fasta,gene_bed,gff,gtf,hisat2_index,kallisto_index,rsem_index,salmon_index,star_index,transcript_fasta'
     validationShowHiddenParams       = false
     validate_params                  = true
 

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -1,12 +1,12 @@
 {
     "software_versions": {
         "content": [
-            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={r-base=4.2.1, bioconductor-dupradar=1.28.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.19.2}, SAMTOOLS_IDXSTATS={samtools=1.19.2}, SAMTOOLS_INDEX={samtools=1.19.2}, SAMTOOLS_SORT={samtools=1.19.2}, SAMTOOLS_STATS={samtools=1.19.2}, SE_GENE={r-base=4.3.2, bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={r-base=4.3.2, bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
+            "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.19.2}, SAMTOOLS_IDXSTATS={samtools=1.19.2}, SAMTOOLS_INDEX={samtools=1.19.2}, SAMTOOLS_SORT={samtools=1.19.2}, SAMTOOLS_STATS={samtools=1.19.2}, SE_GENE={r-base=4.3.2, bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={r-base=4.3.2, bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.3}, Workflow={nf-core/rnaseq=v3.15.0dev}}"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.01.0"
         },
         "timestamp": "2024-03-04T12:40:26.161319"
     }
-}
+}