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fix: adjust import paths to re-organization

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This commit is contained in:
Moritz E. Beber 2022-10-05 13:40:43 +02:00
parent b407fbcdce
commit f5af9fd939
12 changed files with 41 additions and 41 deletions
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2
subworkflows/local/db_check.nf
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@ -3,7 +3,7 @@
// //
include { DATABASE_CHECK } from '../../modules/local/database_check' 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 { workflow DB_CHECK {
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4
subworkflows/local/input_check.nf
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@ -2,8 +2,8 @@
// Check input samplesheet and get read channels // Check input samplesheet and get read channels
// //
include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main' include { EIDO_VALIDATE } from '../../modules/nf-core/eido/validate/main'
include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main' include { EIDO_CONVERT } from '../../modules/nf-core/eido/convert/main'
workflow INPUT_CHECK { workflow INPUT_CHECK {
take: take:

8
subworkflows/local/longread_hostremoval.nf
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@ -2,10 +2,10 @@
// Remove host reads via alignment and export off-target reads // Remove host reads via alignment and export off-target reads
// //
include { MINIMAP2_INDEX } from '../../modules/nf-core/modules/minimap2/index/main' include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main'
include { MINIMAP2_ALIGN } from '../../modules/nf-core/modules/minimap2/align/main' include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
include { SAMTOOLS_VIEW } from '../../modules/nf-core/modules/samtools/view/main' include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/modules/samtools/bam2fq/main' include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main'
workflow LONGREAD_HOSTREMOVAL { workflow LONGREAD_HOSTREMOVAL {
take: take:

6
subworkflows/local/longread_preprocessing.nf
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@ -2,9 +2,9 @@
// Process long raw reads with porechop // Process long raw reads with porechop
// //
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main' include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main' include { PORECHOP } from '../../modules/nf-core/porechop/main'
include { FILTLONG } from '../../modules/nf-core/modules/filtlong/main' include { FILTLONG } from '../../modules/nf-core/filtlong/main'
workflow LONGREAD_PREPROCESSING { workflow LONGREAD_PREPROCESSING {
take: take:

18
subworkflows/local/profiling.nf
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@ -2,15 +2,15 @@
// Run profiling // Run profiling
// //
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main' include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/modules/megan/rma2info/main' include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main' include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main' include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main' include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/metaphlan3/main' include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main' include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main' include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main' include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
workflow PROFILING { workflow PROFILING {
take: take:

6
subworkflows/local/shortread_adapterremoval.nf
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@ -2,9 +2,9 @@
// Process short raw reads with AdapterRemoval // Process short raw reads with AdapterRemoval
// //
include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main' include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/adapterremoval/main'
include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main' include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/adapterremoval/main'
include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main' include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main'
workflow SHORTREAD_ADAPTERREMOVAL { workflow SHORTREAD_ADAPTERREMOVAL {

4
subworkflows/local/shortread_complexityfiltering.nf
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@ -2,8 +2,8 @@
// Check input samplesheet and get read channels // Check input samplesheet and get read channels
// //
include { BBMAP_BBDUK } from '../../modules/nf-core/modules/bbmap/bbduk/main' include { BBMAP_BBDUK } from '../../modules/nf-core/bbmap/bbduk/main'
include { PRINSEQPLUSPLUS } from '../../modules/nf-core/modules/prinseqplusplus/main' include { PRINSEQPLUSPLUS } from '../../modules/nf-core/prinseqplusplus/main'
workflow SHORTREAD_COMPLEXITYFILTERING { workflow SHORTREAD_COMPLEXITYFILTERING {
take: take:

4
subworkflows/local/shortread_fastp.nf
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@ -2,8 +2,8 @@
// Process short raw reads with FastP // Process short raw reads with FastP
// //
include { FASTP as FASTP_SINGLE } 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/modules/fastp/main' include { FASTP as FASTP_PAIRED } from '../../modules/nf-core/fastp/main'
workflow SHORTREAD_FASTP { workflow SHORTREAD_FASTP {
take: take:

4
subworkflows/local/shortread_hostremoval.nf
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@ -2,8 +2,8 @@
// Remove host reads via alignment and export off-target reads // Remove host reads via alignment and export off-target reads
// //
include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main' include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main'
include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main' include { BOWTIE2_ALIGN } from '../../modules/nf-core/bowtie2/align/main'
workflow SHORTREAD_HOSTREMOVAL { workflow SHORTREAD_HOSTREMOVAL {
take: take:

2
subworkflows/local/shortread_preprocessing.nf
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@ -5,7 +5,7 @@
include { SHORTREAD_FASTP } from './shortread_fastp' include { SHORTREAD_FASTP } from './shortread_fastp'
include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval' 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 { workflow SHORTREAD_PREPROCESSING {
take: take:

10
subworkflows/local/standardisation_profiles.nf
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@ -2,11 +2,11 @@
// Standardise output files e.g. aggregation // Standardise output files e.g. aggregation
// //
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main' include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/modules/krakentools/combinekreports/main' include { KRAKENTOOLS_COMBINEKREPORTS } from '../../modules/nf-core/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/modules/krakentools/combinekreports/main' include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/modules/metaphlan3/mergemetaphlantables/main' include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
include { MOTUS_MERGE } from '../../modules/nf-core/modules/motus/merge/main' include { MOTUS_MERGE } from '../../modules/nf-core/motus/merge/main'
workflow STANDARDISATION_PROFILES { workflow STANDARDISATION_PROFILES {
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12
subworkflows/local/visualization_krona.nf
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@ -2,13 +2,13 @@
// Create Krona visualizations // Create Krona visualizations
// //
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/modules/megan/rma2info/main' include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/megan/rma2info/main'
include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main' include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/kaiju/kaiju2krona/main'
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main' include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/krakentools/kreport2krona/main'
include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup' include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/modules/krona/ktimporttext/main' include { KRONA_KTIMPORTTEXT } from '../../modules/nf-core/krona/ktimporttext/main'
include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/modules/krona/ktimporttaxonomy/main' include { KRONA_KTIMPORTTAXONOMY } from '../../modules/nf-core/krona/ktimporttaxonomy/main'
include { GUNZIP } from '../../modules/nf-core/modules/gunzip/main' include { GUNZIP } from '../../modules/nf-core/gunzip/main'
workflow VISUALIZATION_KRONA { workflow VISUALIZATION_KRONA {
take: take: