Fix paths in subworkflows

Author: drpatelh

…rkflows/nf-core/bam_trim_primers_ivar.nf …workflows/local/bam_trim_primers_ivar.nfsubworkflows/nf-core/bam_trim_primers_ivar.nf renamed to subworkflows/local/bam_trim_primers_ivar.nf subworkflows/nf-core/bam_trim_primers_ivar.nf renamed to subworkflows/local/bam_trim_primers_ivar.nf

@@ -3,7 +3,7 @@
 //
 
 include { IVAR_TRIM               } from '../../modules/nf-core/ivar/trim/main'
-include { BAM_SORT_STATS_SAMTOOLS } from './bam_sort_stats_samtools/main'
+include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main'
 
 workflow BAM_TRIM_PRIMERS_IVAR {
     take:

…flows/nf-core/fastq_trim_fastp_fastqc.nf …rkflows/local/fastq_trim_fastp_fastqc.nfsubworkflows/nf-core/fastq_trim_fastp_fastqc.nf renamed to subworkflows/local/fastq_trim_fastp_fastqc.nf subworkflows/nf-core/fastq_trim_fastp_fastqc.nf renamed to subworkflows/local/fastq_trim_fastp_fastqc.nf

@@ -4,7 +4,7 @@
 
 include { SAMTOOLS_VIEW      } from '../../modules/nf-core/samtools/view/main'
 include { SAMTOOLS_INDEX     } from '../../modules/nf-core/samtools/index/main'
-include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools'
+include { BAM_STATS_SAMTOOLS } from '../nf-core/bam_stats_samtools/main'
 
 workflow FILTER_BAM_SAMTOOLS {
     take:

…workflows/nf-core/filter_bam_samtools.nf subworkflows/local/filter_bam_samtools.nfsubworkflows/nf-core/filter_bam_samtools.nf renamed to subworkflows/local/filter_bam_samtools.nf subworkflows/nf-core/filter_bam_samtools.nf renamed to subworkflows/local/filter_bam_samtools.nf

@@ -5,7 +5,7 @@
 include { SNPEFF_ANN            } from '../../modules/local/snpeff_ann'
 include { SNPSIFT_EXTRACTFIELDS } from '../../modules/local/snpsift_extractfields'
 
-include { VCF_BGZIP_TABIX_STATS } from '../nf-core/vcf_bgzip_tabix_stats'
+include { VCF_BGZIP_TABIX_STATS } from './vcf_bgzip_tabix_stats'
 
 workflow SNPEFF_SNPSIFT {
     take:

subworkflows/local/snpeff_snpsift.nf

@@ -4,7 +4,7 @@
 
 include { BCFTOOLS_MPILEUP } from '../../modules/nf-core/bcftools/mpileup/main'
 include { BCFTOOLS_NORM    } from '../../modules/nf-core/bcftools/norm/main'
-include { VCF_TABIX_STATS  } from '../nf-core/vcf_tabix_stats'
+include { VCF_TABIX_STATS  } from './vcf_tabix_stats'
 include { VARIANTS_QC      } from './variants_qc'
 
 workflow VARIANTS_BCFTOOLS {

subworkflows/local/variants_bcftools.nf

@@ -5,7 +5,7 @@
 include { IVAR_VARIANTS         } from '../../modules/nf-core/ivar/variants/main'
 include { IVAR_VARIANTS_TO_VCF  } from '../../modules/local/ivar_variants_to_vcf'
 include { BCFTOOLS_SORT         } from '../../modules/nf-core/bcftools/sort/main'
-include { VCF_TABIX_STATS       } from '../nf-core/vcf_tabix_stats'
+include { VCF_TABIX_STATS       } from './vcf_tabix_stats'
 include { VARIANTS_QC           } from './variants_qc'
 
 workflow VARIANTS_IVAR {

subworkflows/local/variants_ivar.nf

@@ -63,16 +63,18 @@ include { PLOT_MOSDEPTH_REGIONS as PLOT_MOSDEPTH_REGIONS_AMPLICON } from '../mod
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { INPUT_CHECK         } from '../subworkflows/local/input_check'
-include { PREPARE_GENOME      } from '../subworkflows/local/prepare_genome_illumina'
-include { VARIANTS_IVAR       } from '../subworkflows/local/variants_ivar'
-include { VARIANTS_BCFTOOLS   } from '../subworkflows/local/variants_bcftools'
-include { CONSENSUS_IVAR      } from '../subworkflows/local/consensus_ivar'
-include { CONSENSUS_BCFTOOLS  } from '../subworkflows/local/consensus_bcftools'
-include { VARIANTS_LONG_TABLE } from '../subworkflows/local/variants_long_table'
-include { ASSEMBLY_SPADES     } from '../subworkflows/local/assembly_spades'
-include { ASSEMBLY_UNICYCLER  } from '../subworkflows/local/assembly_unicycler'
-include { ASSEMBLY_MINIA      } from '../subworkflows/local/assembly_minia'
+include { INPUT_CHECK             } from '../subworkflows/local/input_check'
+include { PREPARE_GENOME          } from '../subworkflows/local/prepare_genome_illumina'
+include { VARIANTS_IVAR           } from '../subworkflows/local/variants_ivar'
+include { VARIANTS_BCFTOOLS       } from '../subworkflows/local/variants_bcftools'
+include { CONSENSUS_IVAR          } from '../subworkflows/local/consensus_ivar'
+include { CONSENSUS_BCFTOOLS      } from '../subworkflows/local/consensus_bcftools'
+include { VARIANTS_LONG_TABLE     } from '../subworkflows/local/variants_long_table'
+include { ASSEMBLY_SPADES         } from '../subworkflows/local/assembly_spades'
+include { ASSEMBLY_UNICYCLER      } from '../subworkflows/local/assembly_unicycler'
+include { ASSEMBLY_MINIA          } from '../subworkflows/local/assembly_minia'
+include { BAM_TRIM_PRIMERS_IVAR   } from '../subworkflows/local/bam_trim_primers_ivar'
+include { FASTQ_TRIM_FASTP_FASTQC } from '../subworkflows/local/fastq_trim_fastp_fastqc'
 
 /*
 ========================================================================================
@@ -94,9 +96,7 @@ include { MOSDEPTH as MOSDEPTH_AMPLICON } from '../modules/nf-core/mosdepth/main
 //
 // SUBWORKFLOW: Consisting entirely of nf-core/modules
 //
-include { FASTQ_TRIM_FASTP_FASTQC   } from '../subworkflows/nf-core/fastq_trim_fastp_fastqc'
 include { FASTQ_ALIGN_BOWTIE2       } from '../subworkflows/nf-core/fastq_align_bowtie2/main'
-include { BAM_TRIM_PRIMERS_IVAR     } from '../subworkflows/nf-core/bam_trim_primers_ivar'
 include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_markduplicates_picard'
 
 /*

…rkflows/nf-core/vcf_bgzip_tabix_stats.nf …workflows/local/vcf_bgzip_tabix_stats.nfsubworkflows/nf-core/vcf_bgzip_tabix_stats.nf renamed to subworkflows/local/vcf_bgzip_tabix_stats.nf subworkflows/nf-core/vcf_bgzip_tabix_stats.nf renamed to subworkflows/local/vcf_bgzip_tabix_stats.nf

@@ -62,6 +62,7 @@ include { INPUT_CHECK         } from '../subworkflows/local/input_check'
 include { PREPARE_GENOME      } from '../subworkflows/local/prepare_genome_nanopore'
 include { SNPEFF_SNPSIFT      } from '../subworkflows/local/snpeff_snpsift'
 include { VARIANTS_LONG_TABLE } from '../subworkflows/local/variants_long_table'
+include { FILTER_BAM_SAMTOOLS } from '../subworkflows/local/filter_bam_samtools'
 
 /*
 ========================================================================================
@@ -86,11 +87,6 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS   } from '../modules/nf-core/custom/dumpso
 include { MOSDEPTH as MOSDEPTH_GENOME   } from '../modules/nf-core/mosdepth/main'
 include { MOSDEPTH as MOSDEPTH_AMPLICON } from '../modules/nf-core/mosdepth/main'
 
-//
-// SUBWORKFLOW: Consisting entirely of nf-core/modules
-//
-include { FILTER_BAM_SAMTOOLS } from '../subworkflows/nf-core/filter_bam_samtools'
-
 /*
 ========================================================================================
     RUN MAIN WORKFLOW