luslab-umitools | Module feature complete

This commit is contained in:
Chris Cheshire 2020-06-19 08:21:55 +01:00
parent 436d6a6292
commit 9945ac88e0
4 changed files with 49 additions and 45 deletions

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@ -1,38 +0,0 @@
name: HISAT2
description: Graph-based alignment of next generation sequencing reads to a population of genomes
keywords:
- Alignment
- Short reads
- graph FM Index (GFM)
- RNA-seq
tools:
- fastqc:
description: |
HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (whole-genome, transcriptome, and exome sequencing data)
against the general human population (as well as against a single reference genome).
Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
graph FM index (GFM).
homepage: http://daehwankimlab.github.io/hisat2/
documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
input:
-
- sample_id:
type: string
description: Sample identifier
- reads:
type: file
description: Input FastQ file, or pair of files
output:
-
- report:
type: file
description: mapping statistics report
pattern: *hisat2_stats.txt
- alignment:
type: file
description: alignment file in BAM format
pattern: *hisat2.bam
authors:
- @FelixKrueger

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@ -17,7 +17,8 @@ process umitools_dedup {
tuple val(sample_id), path(bai), path(bam) tuple val(sample_id), path(bai), path(bam)
output: output:
tuple val(sample_id), path(bam), emit: dedupBam tuple val(sample_id), path("*.dedup.bam"), emit: dedupBam
path "*.dedup.log", emit: report
shell: shell:
@ -30,16 +31,17 @@ process umitools_dedup {
// Check main args string exists and strip whitespace // Check main args string exists and strip whitespace
if(params.umitools_dedup_args) { if(params.umitools_dedup_args) {
internal_args = params.umitools_dedup_args internal_args = params.umitools_dedup_args
internal_args = internal_args.trim() + " " internal_args = internal_args.trim() + " --log=${sample_id}.dedup.log "
args_exist = "true" args_exist = "true"
} }
else { else {
error_message = "params.umitools_dedup_args does not exist, please define to run this module." error_message = "params.umitools_dedup_args does not exist, please define to run this module."
} }
//SHELL
""" """
if ${args_exist}; then if ${args_exist}; then
${internal_prog}${internal_args}-I $bam ${internal_prog}${internal_args}-I $bam -S ${sample_id}.dedup.bam --output-stats=${sample_id}
else else
echo "${error_message}" 1>&2 echo "${error_message}" 1>&2
exit 1 exit 1

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@ -23,10 +23,6 @@ include umitools_dedup from '../main.nf'
/* Define input channels /* Define input channels
--------------------------------------------------------------------------------------*/ --------------------------------------------------------------------------------------*/
//fileName=`basename $bam`
// sampleName="\${fileName%.Aligned.sortedByCoord.out.bam}"
// umi_tools dedup --umi-separator=":" -I $bam -S \${sampleName}.dedup.bam --output-stats=\${sampleName}
// Meta data // Meta data
testMetaDataBam = [ testMetaDataBam = [
['sample1', "$baseDir/input/sample1.bam"], ['sample1', "$baseDir/input/sample1.bam"],

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@ -0,0 +1,44 @@
name: umi_tools
version: 1.0
description: Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
keywords:
- UMI
- RMT
- Barcode
tools:
- umi_tools:
description: |
Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
homepage: https://github.com/CGATOxford/UMI-tools
documentation: https://umi-tools.readthedocs.io/en/latest/
processes:
- dedup:
opperation: |
Set command args to params.umitools_dedup_args
The program will execute with the following pattern: umi_tools dedeup ARGS -I $bam -S SAMPLE_ID.dedup.bam --output-stats=SAMPLE_ID
description: |
Groups PCR duplicates and deduplicates reads to yield one read per group.
Use this when you want to remove the PCR duplicates prior to any downstream analysis.
input:
- sample_id:
type: string
description: Sample identifier
- bai:
type: file
description: BAM file index
- bam:
type: file
description: BAM sequence file
output:
- dedupBam:
type: tuple
description: A tuple of samples id and output bam file
pattern: *SAMPLE_ID.dedup.bam
- report:
type: file
description: Log file for the umi_tools opperation
pattern: *SAMPLE_ID.dedup.log
authors:
- @candiceh08
- @chris-cheshire