Skip to content

Commit 8f63b05

Browse files
matthdsmmatthdsm
authored
Merge pull request #106 from nf-cmgg/dev
Release v2.0.2 PR
2 parents 12716c7 + a5a2e83 commit 8f63b05

95 files changed

Lines changed: 807 additions & 1885 deletions

File tree

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎.github/workflows/ci.yml‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,7 @@ jobs:
3030
strategy:
3131
matrix:
3232
NXF_VER:
33-
- "24.04.2"
34-
- "latest-everything"
33+
- "24.04.4"
3534
tags:
3635
- "modules/local/panelcoverage"
3736
- "subworkflows/local/bam_qc"

‎CHANGELOG.md‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,16 @@
33
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
44
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
55

6+
## dev
7+
8+
## v2.0.2
9+
10+
- Drop unsed params
11+
- Set aligner to `star` for RNA-seq
12+
- Finetune resources
13+
- Fix some bugs for different input tags
14+
- Update modules
15+
616
## v2.0.1
717

818
- Fix syntax according to new rules

‎assets/multiqc_config.yml‎

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
report_comment: >
2-
This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/2.0.1" target="_blank">nf-cmgg/preprocessing</a>
2+
This report has been generated by the <a href="https://github.com/nf-cmgg/preprocessing/releases/tag/2.0.2" target="_blank">nf-cmgg/preprocessing</a>
33
analysis pipeline.
44
report_section_order:
55
"nf-cmgg-preprocessing-methods-description":
@@ -23,6 +23,17 @@ mosdepth_config:
2323
- "HLA*"
2424
- "chrM"
2525
- "chrEBV"
26+
samtools_coverage:
27+
include_contigs:
28+
- "chr*"
29+
exclude_contigs:
30+
- "*_alt"
31+
- "*_decoy"
32+
- "*_random"
33+
- "chrUn*"
34+
- "HLA*"
35+
- "chrM"
36+
- "chrEBV"
2637
extra_fn_clean_exts:
2738
- ".cram"
2839
- ".coverage"

‎assets/schema_input.json‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,7 @@
2323
"meta": ["organism"],
2424
"type": "string",
2525
"description": "Sample organism. Currently supported organisms include Homo sapiens, Mus musculus and Danio rerio",
26-
"pattern": "^[a-zA-Z0-9_\\s]+$",
27-
"enum": ["Homo sapiens", "Mus musculus", "Danio rerio"]
26+
"pattern": "^[a-zA-Z0-9_\\s]+$"
2827
},
2928
"genome": {
3029
"meta": ["genome"],

‎assets/schema_sampleinfo.json‎

Lines changed: 7 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -42,16 +42,7 @@
4242
"meta": ["organism"],
4343
"type": "string",
4444
"description": "Sample organism",
45-
"pattern": "^[a-zA-Z0-9_\\s]+$",
46-
"enum": [
47-
"Homo sapiens",
48-
"Mus musculus",
49-
"Danio rerio",
50-
"SarsCov",
51-
"Mus Musculus",
52-
"Homo Sapiens",
53-
"Danio Rerio"
54-
]
45+
"pattern": "^[a-zA-Z0-9_\\s]+$"
5546
},
5647
"genome": {
5748
"meta": ["genome"],
@@ -89,6 +80,12 @@
8980
"description": "Region of interest BED file for coverage analysis",
9081
"pattern": "^[a-zA-Z0-9_]+.bed$",
9182
"default": null
83+
},
84+
"aligner": {
85+
"meta": ["aligner"],
86+
"type": "string",
87+
"description": "Aligner to use to align sample to the reference genome",
88+
"enum": ["bowtie2", "bwamem", "bwamem2", "dragmap", "snap", "star"]
9289
}
9390
}
9491
},

‎conf/base.config‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -30,17 +30,17 @@ process {
3030
time = { 4.h * task.attempt }
3131
}
3232
withLabel:process_medium {
33-
cpus = { 9 * task.attempt }
34-
memory = { 72.GB * task.attempt }
33+
cpus = { 8 * task.attempt }
34+
memory = { 64.GB * task.attempt }
3535
time = { 8.h * task.attempt }
3636
}
3737
withLabel:process_high {
38-
cpus = { 18 * task.attempt }
39-
memory = { 144.GB * task.attempt }
38+
cpus = { 16 * task.attempt }
39+
memory = { 128.GB * task.attempt }
4040
time = { 16.h * task.attempt }
4141
}
4242
withLabel:process_long {
43-
time = { 20.h * task.attempt }
43+
time = { 72.h * task.attempt }
4444
}
4545
withLabel:process_high_memory {
4646
memory = { 200.GB * task.attempt }

‎conf/igenomes.config‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@ params {
2727

2828
// ROI's
2929
roi_copgt = "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_coPGT-M_analyses_ROI_v1.bed"
30+
roi_wes = "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v5.bed"
3031
}
3132
"GRCm39" {
3233
// Genome reference

‎conf/modules.config‎

Lines changed: 6 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -20,8 +20,6 @@ process {
2020

2121
// BCL convert
2222
withName: BCLCONVERT {
23-
cpus = 18
24-
memory = 144.GB
2523
ext.args = {[
2624
meta.lane ? "--bcl-only-lane ${meta.lane}" : "",
2725
"--force",
@@ -80,6 +78,7 @@ process {
8078
params.trim_tail > 0 ? "--trim_tail1 ${params.trim_tail}" : "",
8179
params.adapter_R1 ? "--adapter_sequence ${params.adapter_R1}" : "",
8280
params.adapter_R2 ? "--adapter_sequence_r2 ${params.adapter_R2}" : "",
81+
"--compression 1"
8382
].join(" ").trim()}
8483
publishDir = [
8584
[
@@ -93,8 +92,7 @@ process {
9392
// FASTQ_TO_UCRAM
9493
//// Samtools Import
9594
withName: ".*FASTQ_TO_UCRAM:SAMTOOLS_IMPORT" {
96-
cpus = 9
97-
memory = { 36.GB * task.attempt }
95+
label = "process_medium"
9896
// WARNING: Do NOT escape the RG tag tabs when adding a readgroup
9997
ext.args = {[
10098
meta.readgroup ? "--rg-line \"@RG\t" + meta.readgroup.findResults{ it.value?.trim() ? "$it.key:$it.value" : null }.join("\t") + "\"" : "",
@@ -104,11 +102,6 @@ process {
104102
publishDir = [ enabled: false ]
105103
}
106104

107-
withName: ".*FASTQ_TO_UCRAM:SAMTOOLS_CAT" {
108-
cpus = 9
109-
memory = { 36.GB * task.attempt }
110-
}
111-
112105
// FASTQ_TO_CRAM
113106
// Readgroup
114107
// Example:
@@ -204,7 +197,8 @@ process {
204197
"--chimSegmentMin 20",
205198
// alignment will be output only if it has no more mismatches than this value.
206199
"--outFilterMismatchNmax 4",
207-
meta.readgroup ? "--outSAMattrRGline " + meta.readgroup.findResults{ it.value?.trim() ? "$it.key:$it.value" : null }.join(" ") + "\"" : ""
200+
// set the readgroup info, if available. Flag arg MUST start with 'ID' tag
201+
meta.readgroup ? "--outSAMattrRGline \"ID:${meta.readgroup.ID}" + meta.readgroup.findResults{ it.value?.trim() && it.key != "ID" ? "$it.key:$it.value" : null }.join(" ") + "\"" : ""
208202
].join(" ").trim()}
209203
}
210204

@@ -273,6 +267,7 @@ process {
273267

274268
//// Samtools convert
275269
withName: ".*FASTQ_TO_CRAM:SAMTOOLS_CONVERT" {
270+
label = "process_medium"
276271
ext.args = {[
277272
"-C",
278273
"--output-fmt cram",
@@ -292,6 +287,7 @@ process {
292287
//// Mosdepth
293288
withName: ".*COVERAGE:MOSDEPTH" {
294289
cpus = 4
290+
memory = { 4.GB * task.attempt }
295291
// filter reads with flag 1804
296292
// read unmapped (0x4)
297293
// mate unmapped (0x8)*

‎conf/profiles/WES.config‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
params {
2-
genome = "GRCh38"
32
aligner = "snap"
43
run_coverage = true
54
disable_picard_metrics = false
5+
roi = "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v5.bed"
66
}

‎conf/profiles/WGS.config‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
11
params {
2-
genome = "GRCh38"
32
aligner = "snap"
43
run_coverage = true
54
disable_picard_metrics = false

0 commit comments

Comments
 (0)