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nf-core · Oct 11, 2023 · ed219ad · ed219ad
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diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
@@ -2,9 +2,9 @@
 // Alignment with STAR
 //
 
-include { STAR_ALIGN              } from '../../../modules/nf-core/star/align/main'
-include { STAR_ALIGN_IGENOMES     } from '../../../modules/local/star_align_igenomes/main'
-include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools/main'
+include { STAR_ALIGN              } from '../../../modules/nf-core/star/align'
+include { STAR_ALIGN_IGENOMES     } from '../../../modules/local/star_align_igenomes'
+include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools'
 
 workflow ALIGN_STAR {
     take:

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
@@ -2,34 +2,34 @@
 // Uncompress and prepare reference genome files
 //
 
-include { GUNZIP as GUNZIP_FASTA            } from '../../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GTF              } from '../../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GFF              } from '../../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GENE_BED         } from '../../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip/main'
+include { GUNZIP as GUNZIP_FASTA            } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GTF              } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GFF              } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GENE_BED         } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip'
 
-include { UNTAR as UNTAR_BBSPLIT_INDEX      } from '../../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_STAR_INDEX         } from '../../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_RSEM_INDEX         } from '../../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_HISAT2_INDEX       } from '../../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_SALMON_INDEX       } from '../../../modules/nf-core/untar/main'
+include { UNTAR as UNTAR_BBSPLIT_INDEX      } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_STAR_INDEX         } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_RSEM_INDEX         } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_HISAT2_INDEX       } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_SALMON_INDEX       } from '../../../modules/nf-core/untar'
 
-include { CUSTOM_GETCHROMSIZES              } from '../../../modules/nf-core/custom/getchromsizes/main'
-include { GFFREAD                           } from '../../../modules/nf-core/gffread/main'
-include { BBMAP_BBSPLIT                     } from '../../../modules/nf-core/bbmap/bbsplit/main'
-include { STAR_GENOMEGENERATE               } from '../../../modules/nf-core/star/genomegenerate/main'
-include { HISAT2_EXTRACTSPLICESITES         } from '../../../modules/nf-core/hisat2/extractsplicesites/main'
-include { HISAT2_BUILD                      } from '../../../modules/nf-core/hisat2/build/main'
-include { SALMON_INDEX                      } from '../../../modules/nf-core/salmon/index/main'
-include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference/main'
-include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA       } from '../../../modules/nf-core/rsem/preparereference/main'
+include { CUSTOM_GETCHROMSIZES              } from '../../../modules/nf-core/custom/getchromsizes'
+include { GFFREAD                           } from '../../../modules/nf-core/gffread'
+include { BBMAP_BBSPLIT                     } from '../../../modules/nf-core/bbmap/bbsplit'
+include { STAR_GENOMEGENERATE               } from '../../../modules/nf-core/star/genomegenerate'
+include { HISAT2_EXTRACTSPLICESITES         } from '../../../modules/nf-core/hisat2/extractsplicesites'
+include { HISAT2_BUILD                      } from '../../../modules/nf-core/hisat2/build'
+include { SALMON_INDEX                      } from '../../../modules/nf-core/salmon/index'
+include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference'
+include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA       } from '../../../modules/nf-core/rsem/preparereference'
 
-include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode/main'
-include { GTF2BED                              } from '../../../modules/local/gtf2bed/main'
-include { CAT_ADDITIONAL_FASTA                 } from '../../../modules/local/cat_additional_fasta/main'
-include { GTF_GENE_FILTER                      } from '../../../modules/local/gtf_gene_filter/main'
-include { STAR_GENOMEGENERATE_IGENOMES         } from '../../../modules/local/star_genomegenerate_igenomes/main'
+include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode'
+include { GTF2BED                              } from '../../../modules/local/gtf2bed'
+include { CAT_ADDITIONAL_FASTA                 } from '../../../modules/local/cat_additional_fasta'
+include { GTF_GENE_FILTER                      } from '../../../modules/local/gtf_gene_filter'
+include { STAR_GENOMEGENERATE_IGENOMES         } from '../../../modules/local/star_genomegenerate_igenomes'
 
 workflow PREPARE_GENOME {
     take:

diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf
@@ -2,9 +2,9 @@
 // Gene/transcript quantification with RSEM
 //
 
-include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression/main'
-include { RSEM_MERGE_COUNTS        } from '../../../modules/local/rsem_merge_counts/main'
-include { BAM_SORT_STATS_SAMTOOLS  } from '../../nf-core/bam_sort_stats_samtools/main'
+include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression'
+include { RSEM_MERGE_COUNTS        } from '../../../modules/local/rsem_merge_counts'
+include { BAM_SORT_STATS_SAMTOOLS  } from '../../nf-core/bam_sort_stats_samtools'
 
 workflow QUANTIFY_RSEM {
     take:

diff --git a/subworkflows/local/quantify_salmon/main.nf b/subworkflows/local/quantify_salmon/main.nf
@@ -2,14 +2,14 @@
 // Pseudo-alignment and quantification with Salmon
 //
 
-include { SALMON_QUANT    } from '../../../modules/nf-core/salmon/quant/main'
-include { SALMON_TX2GENE  } from '../../../modules/local/salmon_tx2gene/main'
-include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport/main'
-
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE               } from '../../../modules/local/salmon_summarizedexperiment/main'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment/main'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED        } from '../../../modules/local/salmon_summarizedexperiment/main'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT         } from '../../../modules/local/salmon_summarizedexperiment/main'
+include { SALMON_QUANT    } from '../../../modules/nf-core/salmon/quant'
+include { SALMON_TX2GENE  } from '../../../modules/local/salmon_tx2gene'
+include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport'
+
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE               } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED        } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT         } from '../../../modules/local/salmon_summarizedexperiment'
 
 workflow QUANTIFY_SALMON {
     take:

diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
@@ -86,22 +86,22 @@ ch_biotypes_header_multiqc   = file("$projectDir/assets/multiqc/biotypes_header.
 // MODULE: Loaded from modules/local/
 //
 include { BEDTOOLS_GENOMECOV                 } from '../modules/local/bedtools_genomecov/main'
-include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc/main'
-include { DESEQ2_QC as DESEQ2_QC_RSEM        } from '../modules/local/deseq2_qc/main'
-include { DESEQ2_QC as DESEQ2_QC_SALMON      } from '../modules/local/deseq2_qc/main'
-include { DUPRADAR                           } from '../modules/local/dupradar/main'
-include { MULTIQC                            } from '../modules/local/multiqc/main'
-include { MULTIQC_CUSTOM_BIOTYPE             } from '../modules/local/multiqc_custom_biotype/main'
-include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem/main'
+include { DESEQ2_QC as DESEQ2_QC_STAR_SALMON } from '../modules/local/deseq2_qc'
+include { DESEQ2_QC as DESEQ2_QC_RSEM        } from '../modules/local/deseq2_qc'
+include { DESEQ2_QC as DESEQ2_QC_SALMON      } from '../modules/local/deseq2_qc'
+include { DUPRADAR                           } from '../modules/local/dupradar'
+include { MULTIQC                            } from '../modules/local/multiqc'
+include { MULTIQC_CUSTOM_BIOTYPE             } from '../modules/local/multiqc_custom_biotype'
+include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { PREPARE_GENOME                          } from '../subworkflows/local/prepare_genome/main'
-include { ALIGN_STAR                              } from '../subworkflows/local/align_star/main'
-include { QUANTIFY_RSEM                           } from '../subworkflows/local/quantify_rsem/main'
-include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon/main'
-include { QUANTIFY_SALMON as QUANTIFY_SALMON      } from '../subworkflows/local/quantify_salmon/main'
+include { PREPARE_GENOME                          } from '../subworkflows/local/prepare_genome'
+include { ALIGN_STAR                              } from '../subworkflows/local/align_star'
+include { QUANTIFY_RSEM                           } from '../subworkflows/local/quantify_rsem'
+include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon'
+include { QUANTIFY_SALMON as QUANTIFY_SALMON      } from '../subworkflows/local/quantify_salmon'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~