removed gff file from read_alignment process

functional_tests/functions.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-# Pierre MARTIN
-# IE Genotoul
-# MIAT - INRAe (Toulouse)
-# 2021
+"""----------------------------------------------------------------------------
+  Script Name: functions.py
+  Description: Functions for functional tests
+  Input files: Expected and observed folders
+  Created By:  Pierre Martin
+  Date:        2021-12-16
+-------------------------------------------------------------------------------
+"""
+
+# Metadata
+__author__ = 'Pierre Martin \
+- MIAT - PF Genotoul'
+__copyright__ = 'Copyright (C) 2021 INRAe'
+__license__ = 'GNU General Public License'
+__version__ = '1'
+__email__ = 'support.bioinfo.genotoul@inra.fr'
+__status__ = 'dev'
 
 # Functions of metagwgs functional_tests (main.py)
 try:

functional_tests/main.py

 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-# Pierre MARTIN
-# IE Genotoul
-# MIAT - INRAe (Toulouse)
-# 2021
+"""----------------------------------------------------------------------------
+  Script Name: main.py
+  Description: Do functional tests on observed results using expected results
+  Input files: Expected and observed folders
+  Created By:  Pierre Martin
+  Date:        2021-12-16
+-------------------------------------------------------------------------------
+"""
+
+# Metadata
+__author__ = 'Pierre Martin \
+- MIAT - PF Genotoul'
+__copyright__ = 'Copyright (C) 2021 INRAe'
+__license__ = 'GNU General Public License'
+__version__ = '1'
+__email__ = 'support.bioinfo.genotoul@inra.fr'
+__status__ = 'dev'
 
 # Usage
     ## cd [work_directory]

main.nf

 #!/usr/bin/env nextflow
+/*
+========================================================================================
+                         metagWGS
+========================================================================================
+ metagWGS Analysis Pipeline.
+ #### Homepage / Documentation
+ https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/
+----------------------------------------------------------------------------------------
+*/
+
 nextflow.enable.dsl = 2
 
 include { SHARED as SH } from './subworkflows/shared'
@@ -70,7 +80,7 @@ include { MULTIQC } from './modules/multiqc'
      S07_TAXO_AFFI options:
        --skip_taxo_affi              Skip this step
        --accession2taxid             FTP adress of file prot.accession2taxid.gz. Default: "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz".
-       --taxdump                     FTP adress of file taxdump.tar.gz. Default: "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz".
+       --taxdump                     FTP adress of file taxdump.tar.gz. Default: "ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump.tar.gz".
        --taxonomy_dir                Directory if taxdump and accession2taxid already downloaded ("PATH/directory").
 
      Other options:

modules/read_alignment.nf

@@ -3,7 +3,7 @@ process BWA_MEM {
    publishDir "${params.outdir}/05_alignment/05_1_reads_alignment_on_contigs/${sampleId}", mode: 'copy'
 
    input:
-      tuple val(sampleId), path(fna), path(read1), path(read2), path(gff)
+      tuple val(sampleId), path(fna), path(read1), path(read2)
 
    output:
       tuple val(sampleId), path("${sampleId}.sort.bam"), path("${sampleId}.sort.bam.bai"), emit: bam
@@ -21,8 +21,6 @@ process BWA_MEM {
       samtools coverage  ${sampleId}.sort.bam > ${sampleId}_coverage.tsv
 
       samtools idxstats ${sampleId}.sort.bam > ${sampleId}.sort.bam.idxstats
-
-      # awk 'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}' ${sampleId}.sort.bam.idxstats > ${sampleId}_contig.bed
       """
 }
 

nextflow.config

@@ -57,8 +57,8 @@ params {
     // Others parameters.
     outdir = "results"
     databases = "databases"
-    accession2taxid = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz"
-    taxdump = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
+    accession2taxid = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz"
+    taxdump = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump.tar.gz"
     taxonomy_dir = false
     hifi_multiqc_config = "$baseDir/assets/hifi_multiqc_config.yaml"
     sr_multiqc_config = "$baseDir/assets/sr_multiqc_config.yaml"

subworkflows/shared.nf

@@ -30,7 +30,6 @@ workflow SHARED {
 
         ch_contigs_and_reads = ch_prokka_fna
             .join(reads, remainder: true)
-            .join(ch_prokka_gff, remainder: true)
 		ch_prot_length = S04_STRUCTURAL_ANNOT.out.prot_length
 	}