From 4b0a2fe37b332786a8ca96727cf130cf02300c96 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 19 Dec 2022 17:36:51 +0100
Subject: [PATCH] [MODIF] update local modules
---
bin/check_samplesheet.py | 2 +-
conf/modules.config | 8 +++++++-
modules/local/hicpro/bowtie2_merge.nf | 2 +-
modules/local/hicpro/build_contact_maps.nf | 13 +++++++------
modules/local/hicpro/combine_mates.nf | 2 +-
modules/local/hicpro/merge_stats.nf | 1 +
modules/local/hicpro/run_ice.nf | 2 +-
modules/local/multiqc.nf | 8 ++++----
modules/local/split_cooler_dump.nf | 9 +++++++--
subworkflows/local/hicpro.nf | 1 +
subworkflows/local/input_check.nf | 1 -
workflows/hic.nf | 1 +
12 files changed, 32 insertions(+), 18 deletions(-)
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 59af511..c498ef4 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -126,7 +126,7 @@ class RowChecker:
for row in self.modified:
sample = row[self._sample_col]
seen[sample] += 1
- row[self._sample_col] = f"{sample}_T{seen[sample]}"
+ ##row[self._sample_col] = f"{sample}_T{seen[sample]}"
def read_head(handle, num_lines=10):
diff --git a/conf/modules.config b/conf/modules.config
index 6a5ccd5..031e7c6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -163,6 +163,7 @@ process {
mode: 'copy',
enabled: params.hicpro_maps
]
+ ext.prefix = { "${meta.id}.${resolution}" }
}
withName: 'ICE_NORMALIZATION' {
@@ -193,6 +194,7 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
mode: 'copy'
]
+ ext.prefix={ "cooler_bins_${cool_bin}" }
}
withName: 'COOLER_CLOAD' {
@@ -202,6 +204,7 @@ process {
mode: 'copy',
enabled : params.save_raw_maps
]
+ ext.prefix = { "${meta.id}.${cool_bin}" }
ext.args = "pairs -c1 2 -p1 3 -c2 4 -p2 5"
}
@@ -212,7 +215,7 @@ process {
mode: 'copy'
]
ext.args = '--force'
- ext.prefix = { "${meta.id}_balanced" }
+ ext.prefix = { "${cool.baseName}_balanced" }
}
withName: 'COOLER_DUMP' {
@@ -258,6 +261,7 @@ process {
mode: 'copy'
]
ext.args = '--bigwig'
+ ext.prefix = { "${meta.id}.${resolution}" }
}
//********************************
@@ -270,6 +274,7 @@ process {
mode: 'copy'
]
ext.args = '15 25 50 --window-pixels'
+ ext.prefix = { "${meta.id}.${resolution}" }
}
withName: 'HIC_FIND_TADS' {
@@ -279,5 +284,6 @@ process {
mode: 'copy'
]
ext.args = '--correctForMultipleTesting fdr'
+ ext.prefix = { "${meta.id}.${resolution}" }
}
}
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index ed200d6..ed6817c 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/modules/local/hicpro/bowtie2_merge.nf
@@ -1,5 +1,5 @@
process MERGE_BOWTIE2{
- tag "$prefix"
+ tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index 097ff59..18ed243 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/modules/local/hicpro/build_contact_maps.nf
@@ -1,5 +1,5 @@
process BUILD_CONTACT_MAPS{
- tag "$meta.id - $res"
+ tag "${meta.id}"
label 'process_high_memory'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
@@ -8,19 +8,20 @@ process BUILD_CONTACT_MAPS{
'ubuntu:20.04' }"
input:
- tuple val(meta), path(vpairs), val(res)
- path chrsize
+ tuple val(meta), path(vpairs), val(resolution)
+ tuple val(meta2), path(chrsize)
output:
- tuple val(meta), val(res), path("*.matrix"), path("*.bed"), emit: maps
+ tuple val(meta), val(resolution), path("*.matrix"), path("*.bed"), emit: maps
script:
+ def prefix = task.ext.prefix ?: "${meta.id}"
"""
build_matrix \\
--matrix-format upper \\
- --binsize ${res} \\
+ --binsize ${resolution} \\
--chrsizes ${chrsize} \\
--ifile ${vpairs} \\
- --oprefix ${meta.id}_${res}
+ --oprefix ${prefix}
"""
}
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index 83b18dc..c0a8063 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/modules/local/hicpro/combine_mates.nf
@@ -1,5 +1,5 @@
process COMBINE_MATES {
- tag "$prefix"
+ tag "${meta.id}"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::pysam=0.19.0" : null)
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index 743f374..757ec23 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/modules/local/hicpro/merge_stats.nf
@@ -1,4 +1,5 @@
process MERGE_STATS {
+ tag "${meta.id}"
label 'process_low'
conda (params.enable_conda ? "conda-forge::python=3.9" : null)
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index 996baf1..bf9bf6e 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/modules/local/hicpro/run_ice.nf
@@ -1,5 +1,5 @@
process ICE_NORMALIZATION{
- tag "$rmaps"
+ tag "${meta.id}"
label 'process_high_memory'
conda (params.enable_conda ? "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" : null)
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 8fa76a1..8af7656 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_medium'
- conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+ conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
input:
path multiqc_config
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index 38e7357..b7272e8 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -2,12 +2,17 @@ process SPLIT_COOLER_DUMP {
tag "$meta.id"
label 'process_low'
+ conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+ 'ubuntu:20.04' }"
+
input:
tuple val(meta), path(bedpe)
output:
- path "*.txt", emit: matrix
- path "versions.yml", emit: versions
+ tuple val(meta), path("*.txt"), emit: matrix
+ path ("versions.yml"), emit: versions
script:
def args = task.ext.args ?: ''
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index 8b106a0..60f99e0 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -72,6 +72,7 @@ workflow HICPRO {
//if (params.split_fastq){
ch_valid_pairs = ch_valid_pairs.map{ it -> removeChunks(it)}.groupTuple()
+ ch_valid_pairs.view()
ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.map{it->removeChunks(it)}.groupTuple()
.concat(HICPRO_MAPPING.out.pairstats.map{it->removeChunks(it)}.groupTuple(),
ch_valid_stats.map{it->removeChunks(it)}.groupTuple())
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index 9735a49..3f21f1f 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -9,7 +9,6 @@ workflow INPUT_CHECK {
samplesheet // file: /path/to/samplesheet.csv
main:
-
if (params.split_fastq){
SAMPLESHEET_CHECK ( samplesheet )
diff --git a/workflows/hic.nf b/workflows/hic.nf
index d5ba119..0f39687 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -184,6 +184,7 @@ workflow HIC {
//
// SUB-WORFLOW: HiC-Pro
//
+ INPUT_CHECK.out.reads.view()
HICPRO (
INPUT_CHECK.out.reads,
PREPARE_GENOME.out.index,
--
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