updates on DSL2

main.nf

@@ -45,7 +45,7 @@ include {
     extract_fastq;
     extract_fastq_from_dir;
     has_extension
-} from './modules/local/functions'
+} from './modules/local/custom/functions'
 
 /*
 ================================================================================
@@ -252,12 +252,10 @@ if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works
 ================================================================================
 */
 
-include { BWAMEM2_MEM }           from './modules/local/bwamem2_mem.nf'
-include { GET_SOFTWARE_VERSIONS } from './modules/local/get_software_versions'
-include { OUTPUT_DOCUMENTATION }  from './modules/local/output_documentation'
-include { TRIM_GALORE }           from './modules/local/trim_galore.nf'
-include { MERGE_BAM_MAPPED }      from './modules/local/merge_mapped_bam' 
-include { MARK_DUPLICATES }       from './modules/local/mark_duplicates' addParams(skip_qc: skip_qc)
+include { BWAMEM2_MEM }           from './modules/local/process/bwamem2_mem.nf'
+include { GET_SOFTWARE_VERSIONS } from './modules/local/process/get_software_versions'
+include { OUTPUT_DOCUMENTATION }  from './modules/local/process/output_documentation'
+include { MERGE_BAM_MAPPED }      from './modules/local/process/merge_mapped_bam' 
 //include { BASE_RECALIBRATION }    from './modules/local/base_recalibration' params(params)
 
 /*
@@ -266,16 +264,18 @@ include { MARK_DUPLICATES }       from './modules/local/mark_duplicates' addPara
 ================================================================================
 */
 
-include { BUILD_INDICES } from './modules/subworkflows/build_indices'
+include { BUILD_INDICES } from './modules/local/subworkflow/build_indices'
 
 /*
 ================================================================================
                         INCLUDE nf-core PIPELINE MODULES
 ================================================================================
 */
 
-include { FASTQC }  from './modules/nf-core/fastqc'
-include { MULTIQC } from './modules/nf-core/multiqc'
+include { TRIM_GALORE }     from './modules/nf-core/software/trim_galore.nf'
+include { MARK_DUPLICATES } from './modules/nf-core/software/mark_duplicates'
+include { FASTQC }          from './modules/nf-core/software/fastqc'
+include { MULTIQC }         from './modules/nf-core/software/multiqc'
 
 // PREPARING CHANNELS FOR PREPROCESSING AND QC
 

modules/local/create_intervals_bed.nf → modules/local/process/create_intervals_bed.nf

@@ -1,4 +1,4 @@
-include { has_extension } from './functions'
+include { has_extension } from '../custom/functions'
 
 process CREATE_INTERVALS_BED {
     tag "${intervals}"

modules/subworkflows/build_indices.nf → modules/local/subworkflow/build_indices.nf

@@ -6,17 +6,17 @@
 
 // And then initialize channels based on params or indexes that were just built
 
-include { BUILD_INTERVALS }                 from '../local/build_intervals.nf'
-include { BWAMEM2_INDEX }                   from '../nf-core/bwamem2_index.nf'
-include { CREATE_INTERVALS_BED }            from '../local/create_intervals_bed.nf'
-include { GATK_CREATE_SEQUENCE_DICTIONARY } from '../local/gatk_dict.nf'
+include { BUILD_INTERVALS }                 from '../../local/process/build_intervals.nf'
+include { BWAMEM2_INDEX }                   from '../../nf-core/software/bwamem2_index.nf'
+include { CREATE_INTERVALS_BED }            from '../../local/process/create_intervals_bed.nf'
+include { GATK_CREATE_SEQUENCE_DICTIONARY } from '../../nf-core/software/gatk_dict.nf'
 include {
     HTSLIB_TABIX as HTSLIB_TABIX_DBSNP;
     HTSLIB_TABIX as HTSLIB_TABIX_GERMLINE_RESOURCE;
     HTSLIB_TABIX as HTSLIB_TABIX_KNOWN_INDELS;
     HTSLIB_TABIX as HTSLIB_TABIX_PON;
-} from '../nf-core/htslib_tabix'
-include { SAMTOOLS_FAIDX }                  from '../nf-core/samtools_faidx.nf'
+} from '../../nf-core/software/htslib_tabix'
+include { SAMTOOLS_FAIDX }                  from '../../nf-core/software/samtools_faidx.nf'
 
 workflow BUILD_INDICES{
     take: