Skip to content

Commit 9e7a128

Browse files
nvnieuwknvnieuwk
authored
Merge pull request #167 from nf-cmgg/feat/parameter_types
Add parameter typing
2 parents 545dd54 + 78b71d8 commit 9e7a128

26 files changed

Lines changed: 4954 additions & 209 deletions

File tree

‎.github/workflows/nf-test.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ concurrency:
1818

1919
env:
2020
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
21-
NFT_VER: "0.9.3"
21+
NFT_VER: "0.9.5"
2222
NFT_WORKDIR: "~"
2323
NXF_ANSI_LOG: false
2424
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -76,7 +76,7 @@ jobs:
7676
- isMain: false
7777
profile: "singularity"
7878
NXF_VER:
79-
- 25.10.0
79+
- 26.04.0
8080
- latest-everything
8181
env:
8282
NXF_ANSI_LOG: false

‎.gitignore‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -9,3 +9,6 @@ testing*
99
null/
1010
.nf-test*
1111
test_fc
12+
# pixi environments
13+
.pixi/*
14+
!.pixi/config.toml

‎.nf-core.yml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@ lint:
2121
- bin/cmgg_genelists
2222
multiqc_config: false
2323
nextflow_config: false
24+
schema_params: false # TMP
2425
template_strings:
2526
- bin/cmgg_genelists
2627
nf_test_content: false

‎.vscode/settings.json‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
11
{
2-
"markdown.styles": ["public/vscode_markdown.css"]
2+
"markdown.styles": ["public/vscode_markdown.css"],
3+
"nextflow.telemetry.enabled": false
34
}

‎CHANGELOG.md‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
55

66
## 3.0.1dev
77

8+
- Add parameter typing to make strict syntax runs work more properly
9+
- Bumped minimal Nextflow version to 26.04.0 to allow for strict syntax and other improvements
810
- Fix an issue with `mosdepth` environment variables not being correctly set on GCP
911
- Bump `mosdepth` module to 0.3.14
1012

‎README.md‎

Lines changed: 11 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
[![GitHub Actions Linting Status](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/preprocessing/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
66
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
77

8-
[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
8+
[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
99
[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
1010
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
1111
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -59,6 +59,16 @@ nextflow run nf-cmgg/preprocessing \
5959
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
6060
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
6161
62+
## Development environment
63+
64+
A [pixi](https://pixi.prefix.dev/latest/) development environment is available for this pipeline. Run the following command to install the environment:
65+
66+
```
67+
pixi install
68+
```
69+
70+
Then run `pixi shell` to enter the environment and start developing.
71+
6272
## Credits
6373

6474
nf-cmgg/preprocessing was originally written by the CMGG ICT team.

‎conf/igenomes.config‎

Lines changed: 86 additions & 88 deletions
Original file line numberDiff line numberDiff line change
@@ -8,98 +8,96 @@
88
----------------------------------------------------------------------------------------
99
*/
1010

11-
params {
12-
genomes {
13-
GRCh38 {
14-
// Genome reference
15-
fai = "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.fai"
16-
fasta = "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna"
17-
dict = "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.dict"
18-
gtf = "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf"
11+
params.genomes = [
12+
GRCh38: [
13+
// Genome reference
14+
fai : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.fai",
15+
fasta : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna",
16+
dict : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.dict",
17+
gtf : "${params.igenomes_base}/Hsapiens/GRCh38/seq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf",
1918

20-
// Aligner reference
21-
bowtie2 = "${params.igenomes_base}/Hsapiens/GRCh38/bowtie2"
22-
bwamem = "${params.igenomes_base}/Hsapiens/GRCh38/bwa"
23-
bwamem2 = "${params.igenomes_base}/Hsapiens/GRCh38/bwamem2"
24-
dragmap = "${params.igenomes_base}/Hsapiens/GRCh38/dragmap"
25-
snap = "${params.igenomes_base}/Hsapiens/GRCh38/snapaligner"
26-
star = "${params.igenomes_base}/Hsapiens/GRCh38/star"
19+
// Aligner reference
20+
bowtie2 : "${params.igenomes_base}/Hsapiens/GRCh38/bowtie2",
21+
bwamem : "${params.igenomes_base}/Hsapiens/GRCh38/bwa",
22+
bwamem2 : "${params.igenomes_base}/Hsapiens/GRCh38/bwamem2",
23+
dragmap : "${params.igenomes_base}/Hsapiens/GRCh38/dragmap",
24+
snap : "${params.igenomes_base}/Hsapiens/GRCh38/snapaligner",
25+
star : "${params.igenomes_base}/Hsapiens/GRCh38/star",
2726

28-
// ROI's
29-
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_v7.bed"
31-
}
32-
GRCm39 {
33-
// Genome reference
34-
fai = "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna.fai"
35-
fasta = "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna"
36-
dict = "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.dict"
37-
gtf = "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.gtf"
27+
// ROI's
28+
roi_copgt : "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_coPGT-M_analyses_ROI_v1.bed",
29+
roi_wes : "${params.igenomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v7.bed",
30+
],
31+
GRCm39: [
32+
// Genome reference
33+
fai : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna.fai",
34+
fasta : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.fna",
35+
dict : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.dict",
36+
gtf : "${params.igenomes_base}/Mmusculus/GRCm39/seq/GCF_000001635.27_GRCm39_genomic.gtf",
3837

39-
// Aligner reference
40-
bowtie2 = "${params.igenomes_base}/Mmusculus/GRCm39/bowtie2"
41-
bwamem = "${params.igenomes_base}/Mmusculus/GRCm39/bwa"
42-
bwamem2 = "${params.igenomes_base}/Mmusculus/GRCm39/bwamem2"
43-
dragmap = "${params.igenomes_base}/Mmusculus/GRCm39/dragmap"
44-
snap = "${params.igenomes_base}/Mmusculus/GRCm39/snapaligner"
45-
star = "${params.igenomes_base}/Mmusculus/GRCm39/star"
46-
}
47-
mm10 {
48-
// Genome reference
49-
fai = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa.fai"
50-
fasta = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa"
51-
dict = "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.dict"
52-
gtf = "${params.igenomes_base}/Mmusculus/mm10/seq/Mus_musculus.GRCm38.102.chr.gtf"
38+
// Aligner reference
39+
bowtie2 : "${params.igenomes_base}/Mmusculus/GRCm39/bowtie2",
40+
bwamem : "${params.igenomes_base}/Mmusculus/GRCm39/bwa",
41+
bwamem2 : "${params.igenomes_base}/Mmusculus/GRCm39/bwamem2",
42+
dragmap : "${params.igenomes_base}/Mmusculus/GRCm39/dragmap",
43+
snap : "${params.igenomes_base}/Mmusculus/GRCm39/snapaligner",
44+
star : "${params.igenomes_base}/Mmusculus/GRCm39/star",
45+
],
46+
mm10: [
47+
// Genome reference
48+
fai : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa.fai",
49+
fasta : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.fa",
50+
dict : "${params.igenomes_base}/Mmusculus/mm10/seq/mm10.dict",
51+
gtf : "${params.igenomes_base}/Mmusculus/mm10/seq/Mus_musculus.GRCm38.102.chr.gtf",
5352

54-
// Aligner reference
55-
bowtie2 = "${params.igenomes_base}/Mmusculus/mm10/bowtie2"
56-
bwamem = "${params.igenomes_base}/Mmusculus/mm10/bwa"
57-
bwamem2 = "${params.igenomes_base}/Mmusculus/mm10/bwamem2"
58-
dragmap = "${params.igenomes_base}/Mmusculus/mm10/dragmap"
59-
snap = "${params.igenomes_base}/Mmusculus/mm10/snapaligner"
60-
star = "${params.igenomes_base}/Mmusculus/mm10/star"
61-
}
62-
GRCz11 {
63-
// Genome reference
64-
fai = "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna.fai"
65-
fasta = "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna"
66-
dict = "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.dict"
67-
gtf = "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.gtf"
53+
// Aligner reference
54+
bowtie2 : "${params.igenomes_base}/Mmusculus/mm10/bowtie2",
55+
bwamem : "${params.igenomes_base}/Mmusculus/mm10/bwa",
56+
bwamem2 : "${params.igenomes_base}/Mmusculus/mm10/bwamem2",
57+
dragmap : "${params.igenomes_base}/Mmusculus/mm10/dragmap",
58+
snap : "${params.igenomes_base}/Mmusculus/mm10/snapaligner",
59+
star : "${params.igenomes_base}/Mmusculus/mm10/star",
60+
],
61+
GRCz11: [
62+
// Genome reference
63+
fai : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna.fai",
64+
fasta : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.fna",
65+
dict : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.dict",
66+
gtf : "${params.igenomes_base}/Drerio/GRCz11/seq/GCF_000002035.6_GRCz11_genomic.gtf",
6867

69-
// Aligner reference
70-
bowtie2 = "${params.igenomes_base}/Drerio/GRCz11/bowtie2"
71-
bwamem = "${params.igenomes_base}/Drerio/GRCz11/bwa"
72-
bwamem2 = "${params.igenomes_base}/Drerio/GRCz11/bwamem2"
73-
dragmap = "${params.igenomes_base}/Drerio/GRCz11/dragmap"
74-
snap = "${params.igenomes_base}/Drerio/GRCz11/snapaligner"
75-
star = "${params.igenomes_base}/Drerio/GRCz11/star"
76-
}
77-
// Legacy bcbio references
78-
hg38 {
79-
fai = "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa.fai"
80-
fasta = "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa"
81-
dict = "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.dict"
82-
gtf = "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.gtf"
68+
// Aligner reference
69+
bowtie2 : "${params.igenomes_base}/Drerio/GRCz11/bowtie2",
70+
bwamem : "${params.igenomes_base}/Drerio/GRCz11/bwa",
71+
bwamem2 : "${params.igenomes_base}/Drerio/GRCz11/bwamem2",
72+
dragmap : "${params.igenomes_base}/Drerio/GRCz11/dragmap",
73+
snap : "${params.igenomes_base}/Drerio/GRCz11/snapaligner",
74+
star : "${params.igenomes_base}/Drerio/GRCz11/star",
75+
],
76+
// Legacy bcbio references
77+
hg38: [
78+
fai : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa.fai",
79+
fasta : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.fa",
80+
dict : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.dict",
81+
gtf : "${params.igenomes_base}/Hsapiens/hg38/seq/hg38.gtf",
8382

84-
bowtie2 = "${params.igenomes_base}/Hsapiens/hg38/bowtie2"
85-
bwamem = "${params.igenomes_base}/Hsapiens/hg38/bwa"
86-
bwamem2 = "${params.igenomes_base}/Hsapiens/hg38/bwamem2"
87-
dragmap = "${params.igenomes_base}/Hsapiens/hg38/dragmap"
88-
snap = "${params.igenomes_base}/Hsapiens/hg38/snapaligner"
89-
star = "${params.igenomes_base}/Hsapiens/hg38/star"
90-
}
91-
'hg38-noalt' {
92-
fai = "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa.fai"
93-
fasta = "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa"
94-
dict = "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.dict"
95-
gtf = "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.gtf"
83+
bowtie2 : "${params.igenomes_base}/Hsapiens/hg38/bowtie2",
84+
bwamem : "${params.igenomes_base}/Hsapiens/hg38/bwa",
85+
bwamem2 : "${params.igenomes_base}/Hsapiens/hg38/bwamem2",
86+
dragmap : "${params.igenomes_base}/Hsapiens/hg38/dragmap",
87+
snap : "${params.igenomes_base}/Hsapiens/hg38/snapaligner",
88+
star : "${params.igenomes_base}/Hsapiens/hg38/star",
89+
],
90+
'hg38-noalt': [
91+
fai : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa.fai",
92+
fasta : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.fa",
93+
dict : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.dict",
94+
gtf : "${params.igenomes_base}/Hsapiens/hg38-noalt/seq/hg38-noalt.gtf",
9695

97-
bowtie2 = "${params.igenomes_base}/Hsapiens/hg38-noalt/bowtie2"
98-
bwamem = "${params.igenomes_base}/Hsapiens/hg38-noalt/bwa"
99-
bwamem2 = "${params.igenomes_base}/Hsapiens/hg38-noalt/bwamem2"
100-
dragmap = "${params.igenomes_base}/Hsapiens/hg38-noalt/dragmap"
101-
snap = "${params.igenomes_base}/Hsapiens/hg38-noalt/snapaligner"
102-
star = "${params.igenomes_base}/Hsapiens/hg38-noalt/star"
103-
}
104-
}
105-
}
96+
bowtie2 : "${params.igenomes_base}/Hsapiens/hg38-noalt/bowtie2",
97+
bwamem : "${params.igenomes_base}/Hsapiens/hg38-noalt/bwa",
98+
bwamem2 : "${params.igenomes_base}/Hsapiens/hg38-noalt/bwamem2",
99+
dragmap : "${params.igenomes_base}/Hsapiens/hg38-noalt/dragmap",
100+
snap : "${params.igenomes_base}/Hsapiens/hg38-noalt/snapaligner",
101+
star : "${params.igenomes_base}/Hsapiens/hg38-noalt/star",
102+
],
103+
]

‎main.nf‎

Lines changed: 104 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,104 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_prep
2222
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2323
*/
2424

25+
params {
26+
27+
// Path to comma-separated or yaml file containing information about the samples in the experiment.
28+
input: Path
29+
30+
// The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
31+
outdir: Path
32+
33+
// Email address for completion summary.
34+
email: String?
35+
36+
// MultiQC report title. Printed as page header, used for filename if not otherwise specified.
37+
multiqc_title: String?
38+
39+
genomes: Map = [:]
40+
41+
// Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.
42+
split_fastq: Integer = 100000000
43+
44+
// Directory containing gene list bed files for granular coverage analysis
45+
genelists: Path?
46+
47+
// Git commit id for Institutional configs.
48+
custom_config_version: String = 'main'
49+
50+
// Base directory for custom configs.
51+
custom_config_base: String = 'https://raw.githubusercontent.com/nf-cmgg/configs/main'
52+
53+
// Institutional config name.
54+
config_profile_name: String?
55+
56+
// Institutional config description.
57+
config_profile_description: String?
58+
59+
// Institutional config contact information.
60+
config_profile_contact: String?
61+
62+
// Institutional config URL link.
63+
config_profile_url: String?
64+
65+
// Display version and exit.
66+
version: Boolean = false
67+
68+
// Method used to save pipeline results to output directory.
69+
publish_dir_mode: String = 'copy'
70+
71+
// Email address for completion summary, only when pipeline fails.
72+
email_on_fail: String?
73+
74+
// Send plain-text email instead of HTML.
75+
plaintext_email: Boolean = false
76+
77+
// File size limit when attaching MultiQC reports to summary emails.
78+
max_multiqc_email_size: String = '25.MB'
79+
80+
// Do not use coloured log outputs.
81+
monochrome_logs: Boolean = false
82+
83+
// Incoming hook URL for messaging service
84+
hook_url: String?
85+
86+
// Custom config file to supply to MultiQC.
87+
multiqc_config: Path?
88+
89+
// Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
90+
multiqc_logo: Path?
91+
92+
// Custom MultiQC yaml file containing HTML including a methods description.
93+
multiqc_methods_description: Path?
94+
95+
// Boolean whether to validate parameters against the schema at runtime
96+
validate_params: Boolean = true
97+
98+
// Base URL or local path to location of pipeline test dataset files
99+
pipelines_testdata_base_path: String = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
100+
101+
// Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
102+
trace_report_suffix: String
103+
104+
// Display the help message.
105+
help = false
106+
107+
// Display the full detailed help message.
108+
help_full: Boolean = false
109+
110+
// Display hidden parameters in the help message (only works when --help or --help_full are provided).
111+
show_hidden: Boolean = false
112+
113+
// Directory / URL base for iGenomes references.
114+
igenomes_base: String = '/references/'
115+
116+
// Do not load the iGenomes reference config.
117+
igenomes_ignore: Boolean = false
118+
119+
// Name of iGenomes reference.
120+
genome: String?
121+
}
122+
25123
workflow {
26124

27125
main:
@@ -47,10 +145,11 @@ workflow {
47145
params.genomes,
48146
params.genelists,
49147
params.multiqc_config
50-
? [file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), file(params.multiqc_config, checkIfExists: true)]
148+
? [file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), params.multiqc_config]
51149
: [file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)],
52-
params.multiqc_logo ? file(params.multiqc_logo, checkIfExists: true) : [],
53-
params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true),
150+
params.multiqc_logo ? params.multiqc_logo : [],
151+
params.multiqc_methods_description ? params.multiqc_methods_description : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true),
152+
params.outdir
54153
)
55154

56155
//
@@ -70,8 +169,8 @@ workflow {
70169
demultiplex_logs = PREPROCESSING.out.demultiplex_logs.transpose()
71170
demultiplex_fastq = PREPROCESSING.out.demultiplex_fastq.transpose()
72171
demultiplex_interop = PREPROCESSING.out.demultiplex_interop.transpose(by: 1)
73-
falco_html = PREPROCESSING.out.falco_html
74-
falco_txt = PREPROCESSING.out.falco_txt
172+
falco_html = PREPROCESSING.out.falco_html.transpose()
173+
falco_txt = PREPROCESSING.out.falco_txt.transpose()
75174
fastp_json = PREPROCESSING.out.fastp_json
76175
fastp_html = PREPROCESSING.out.fastp_html
77176
crams = PREPROCESSING.out.crams

0 commit comments

Comments
 (0)