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Fix genomes params usage #1240

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merged 4 commits into from
Mar 7, 2024
Merged

Fix genomes params usage #1240

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982e0ba
properly fix genome params usage
maxulysse Mar 7, 2024
34a509c
update CHANGELOG
maxulysse Mar 7, 2024
a893c68
Merge branch 'dev' into fix_params
maxulysse Mar 7, 2024
7412996
update dupradar
maxulysse Mar 7, 2024
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14 changes: 12 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -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

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16 changes: 1 addition & 15 deletions nextflow.config
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Expand Up @@ -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
Expand Down Expand Up @@ -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

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4 changes: 2 additions & 2 deletions tests/main.nf.test.snap
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@@ -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"
}
}
}
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