Fixed pipeline to work with template update

LaurenGonsalves · Feb 27, 2024 · 7086a7e · 7086a7e
1 parent acd9658
commit 7086a7e
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Showing 6 changed files with 15 additions and 19 deletions.
diff --git a/modules/local/metaphlan/sgbtogtdbprofile/main.nf b/modules/local/metaphlan/sgbtogtdbprofile/main.nf
@@ -4,8 +4,8 @@ process METAPHLAN_SGBTOGTDBPROFILE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/metaphlan:4.0.6--pyhca03a8a_0' :
-        'biocontainers/metaphlan:4.0.6--pyhca03a8a_0' }"
+        'https://depot.galaxyproject.org/singularity/metaphlan:4.1.0--pyhca03a8a_0' :
+        'biocontainers/metaphlan:4.1.0--pyhca03a8a_0' }"
 
     input:
     tuple val(meta), path(metaphlan_profile)

diff --git a/modules/nf-core/metaphlan/makedb/main.nf b/modules/nf-core/metaphlan/makedb/main.nf
diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/main.nf b/modules/nf-core/metaphlan/mergemetaphlantables/main.nf
diff --git a/modules/nf-core/metaphlan/metaphlan/main.nf b/modules/nf-core/metaphlan/metaphlan/main.nf
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -16,7 +16,6 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
-                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "schema": "assets/schema_input.json",

diff --git a/workflows/biobakerymgx/main.nf b/workflows/biobakerymgx/main.nf
@@ -25,16 +25,16 @@ include { paramsSummaryMap       } from 'plugin/nf-validation'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { FASTQC                 } from '../modules/nf-core/fastqc/main'
+include { FASTQC                 } from '../../modules/nf-core/fastqc/main'
 include { CAT_FASTQ              } from '../../modules/nf-core/cat/fastq/main'
-include { MULTIQC                } from '../modules/nf-core/multiqc/main'
+include { MULTIQC                } from '../../modules/nf-core/multiqc/main'
 
 //
 // SUBWORKFLOWS: Installed directory from nf-core/subworkflows
 //
-include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_biobakerymgx_pipeline'
+include { paramsSummaryMultiqc   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_biobakerymgx_pipeline'
 
 
 
@@ -45,9 +45,6 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_biob
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// Info required for completion email and summary
-def multiqc_report = []
-
 workflow BIOBAKERYMGX {
 
     take:
@@ -63,7 +60,7 @@ workflow BIOBAKERYMGX {
     -----------------------------------------------------------------------------------*/
     if ( !params.skip_runmerging ) {
 
-        ch_reads_for_cat_branch = fastq_gz
+        ch_reads_for_cat_branch = ch_samplesheet
             .map {
                 meta, reads ->
                     def meta_new = meta - meta.subMap('replicate')
@@ -91,7 +88,7 @@ workflow BIOBAKERYMGX {
         ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
 
     } else {
-        ch_reads_runmerged = fastq_gz
+        ch_reads_runmerged = ch_samplesheet
     }
 
     //