Commit 814e6a51 authored by MARTIN Pierre's avatar MARTIN Pierre
Browse files

removed gff file from read_alignment process

parent 1d96308c
#!/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:
......
#!/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]
......
#!/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:
......
......@@ -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 > ${sampleId}_contig.bed
"""
}
......
......@@ -57,8 +57,8 @@ params {
// Others parameters.
outdir = "results"
databases = "databases"
accession2taxid = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz"
taxdump = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
accession2taxid = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz"
taxdump = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump.tar.gz"
taxonomy_dir = false
hifi_multiqc_config = "$baseDir/assets/hifi_multiqc_config.yaml"
sr_multiqc_config = "$baseDir/assets/sr_multiqc_config.yaml"
......
......@@ -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
}
......
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