From f5af9fd939667de6754d0647762eae8d89e0e156 Mon Sep 17 00:00:00 2001 From: "Moritz E. Beber" Date: Wed, 5 Oct 2022 13:40:43 +0200 Subject: [PATCH] fix: adjust import paths to re-organization --- subworkflows/local/db_check.nf | 2 +- subworkflows/local/input_check.nf | 4 ++-- subworkflows/local/longread_hostremoval.nf | 8 ++++---- subworkflows/local/longread_preprocessing.nf | 6 +++--- subworkflows/local/profiling.nf | 18 +++++++++--------- subworkflows/local/shortread_adapterremoval.nf | 6 +++--- .../local/shortread_complexityfiltering.nf | 4 ++-- subworkflows/local/shortread_fastp.nf | 4 ++-- subworkflows/local/shortread_hostremoval.nf | 4 ++-- subworkflows/local/shortread_preprocessing.nf | 2 +- subworkflows/local/standardisation_profiles.nf | 12 ++++++------ subworkflows/local/visualization_krona.nf | 12 ++++++------ 12 files changed, 41 insertions(+), 41 deletions(-) diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf index 7b440c6..5d0c4eb 100644 --- a/subworkflows/local/db_check.nf +++ b/subworkflows/local/db_check.nf @@ -3,7 +3,7 @@ // include { DATABASE_CHECK } from '../../modules/local/database_check' -include { UNTAR } from '../../modules/nf-core/modules/untar/main' +include { UNTAR } from '../../modules/nf-core/untar/main' workflow DB_CHECK { take: diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index e8d5e7a..46baff2 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -2,8 +2,8 @@ // Check input samplesheet and get read channels // -include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main' -include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main' +include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main' +include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main' workflow INPUT_CHECK { take: diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf index 7db020b..5b4413f 100644 --- a/subworkflows/local/longread_hostremoval.nf +++ b/subworkflows/local/longread_hostremoval.nf @@ -2,10 +2,10 @@ // Remove host reads via alignment and export off-target reads // -include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main' -include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main' -include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main' +include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main' +include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main' +include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main' workflow LONGREAD_HOSTREMOVAL { take: diff --git a/subworkflows/local/longread_preprocessing.nf b/subworkflows/local/longread_preprocessing.nf index c04207e..ce537e8 100644 --- a/subworkflows/local/longread_preprocessing.nf +++ b/subworkflows/local/longread_preprocessing.nf @@ -2,9 +2,9 @@ // Process long raw reads with porechop // -include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main' -include { PORECHOP } from '../../modules/nf-core/modules/porechop/main' -include { FILTLONG } from '../../modules/nf-core/modules/filtlong/main' +include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main' +include { PORECHOP } from '../../modules/nf-core/porechop/main' +include { FILTLONG } from '../../modules/nf-core/filtlong/main' workflow LONGREAD_PREPROCESSING { take: diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index c2ef508..11c4a72 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -2,15 +2,15 @@ // Run profiling // -include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main' -include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/modules/megan/rma2info/main' -include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main' -include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main' -include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main' -include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main' -include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main' -include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main' -include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main' +include { MALT_RUN } from '../../modules/nf-core/malt/run/main' +include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main' +include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main' +include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main' +include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main' +include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main' +include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main' +include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main' +include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main' workflow PROFILING { take: diff --git a/subworkflows/local/shortread_adapterremoval.nf b/subworkflows/local/shortread_adapterremoval.nf index e491423..a5a43fe 100644 --- a/subworkflows/local/shortread_adapterremoval.nf +++ b/subworkflows/local/shortread_adapterremoval.nf @@ -2,9 +2,9 @@ // Process short raw reads with AdapterRemoval // -include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main' -include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main' -include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/adapterremoval/main' +include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/adapterremoval/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' workflow SHORTREAD_ADAPTERREMOVAL { diff --git a/subworkflows/local/shortread_complexityfiltering.nf b/subworkflows/local/shortread_complexityfiltering.nf index a34440d..844cd15 100644 --- a/subworkflows/local/shortread_complexityfiltering.nf +++ b/subworkflows/local/shortread_complexityfiltering.nf @@ -2,8 +2,8 @@ // Check input samplesheet and get read channels // -include { BBMAP_BBDUK } from '../../modules/nf-core/modules/bbmap/bbduk/main' -include { PRINSEQPLUSPLUS } from '../../modules/nf-core/modules/prinseqplusplus/main' +include { BBMAP_BBDUK } from '../../modules/nf-core/bbmap/bbduk/main' +include { PRINSEQPLUSPLUS } from '../../modules/nf-core/prinseqplusplus/main' workflow SHORTREAD_COMPLEXITYFILTERING { take: diff --git a/subworkflows/local/shortread_fastp.nf b/subworkflows/local/shortread_fastp.nf index 05e0f3d..d466041 100644 --- a/subworkflows/local/shortread_fastp.nf +++ b/subworkflows/local/shortread_fastp.nf @@ -2,8 +2,8 @@ // Process short raw reads with FastP // -include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/modules/fastp/main' -include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/modules/fastp/main' +include { FASTP as FASTP_SINGLE } from '../../modules/nf-core/fastp/main' +include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/fastp/main' workflow SHORTREAD_FASTP { take: diff --git a/subworkflows/local/shortread_hostremoval.nf b/subworkflows/local/shortread_hostremoval.nf index c5f15c7..d181a34 100644 --- a/subworkflows/local/shortread_hostremoval.nf +++ b/subworkflows/local/shortread_hostremoval.nf @@ -2,8 +2,8 @@ // Remove host reads via alignment and export off-target reads // -include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main' -include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main' +include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main' +include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main' workflow SHORTREAD_HOSTREMOVAL { take: diff --git a/subworkflows/local/shortread_preprocessing.nf b/subworkflows/local/shortread_preprocessing.nf index 977a317..859c1d5 100644 --- a/subworkflows/local/shortread_preprocessing.nf +++ b/subworkflows/local/shortread_preprocessing.nf @@ -5,7 +5,7 @@ include { SHORTREAD_FASTP } from './shortread_fastp' include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval' -include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main' +include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main' workflow SHORTREAD_PREPROCESSING { take: diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index 7a441ff..cbb0fab 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -2,11 +2,11 @@ // Standardise output files e.g. aggregation // -include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main' -include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main' -include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/modules/krakentools/combinekreports/main' -include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/modules/metaphlan3/mergemetaphlantables/main' -include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main' +include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main' +include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main' +include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main' +include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main' +include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main' workflow STANDARDISATION_PROFILES { take: @@ -99,7 +99,7 @@ workflow STANDARDISATION_PROFILES { ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS.out.versions ) // MetaPhlAn3 - + ch_profiles_for_metaphlan3 = ch_input_profiles.metaphlan3 .map { [it[0]['db_name'], it[1]] } .groupTuple() diff --git a/subworkflows/local/visualization_krona.nf b/subworkflows/local/visualization_krona.nf index f06768a..7d8e4f0 100644 --- a/subworkflows/local/visualization_krona.nf +++ b/subworkflows/local/visualization_krona.nf @@ -2,13 +2,13 @@ // Create Krona visualizations // -include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/modules/megan/rma2info/main' -include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main' -include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main' +include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/megan/rma2info/main' +include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/kaiju/kaiju2krona/main' +include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/krakentools/kreport2krona/main' include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup' -include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main' -include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/modules/krona/ktimporttaxonomy/main' -include { GUNZIP } from '../../modules/nf-core/modules/gunzip/main' +include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/krona/ktimporttext/main' +include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/krona/ktimporttaxonomy/main' +include { GUNZIP } from '../../modules/nf-core/gunzip/main' workflow VISUALIZATION_KRONA { take: