Verified Commit 020a69e4 authored by Laurent Modolo's avatar Laurent Modolo
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CONTRIBUTING.md: end of the nf_modules section

parent 2924d6ef
......@@ -118,17 +118,68 @@ process fastp {
Here `file_id` can be anything from a simple identifier to a list of several variables.
So you have to keep that in mind if you want to use it to define output file names (you can test for that with `file_id instanceof List`).
If you want to use information within the `file_id` to name outputs in your `script` section, you can use the following snipet:
```
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
```
and use the `file_prefix` variable.
The rational behind taking a `file_id` and emitting the same `file_id` is to facilitate complex channel operations in pipelines without having to rewrite the `process` blocks.
### dealing with paired-end and single-end data
Fastq files opened with `channel.fromFilePairs( params.fastq )`
Fastq files opened with `channel.fromFilePairs( params.fastq )` create item of the following shape:
```
[file_id, [read_1_file, read_2_file]]
```
To make this call more generic, we can use the `size: -1` option, and accept arbitrary number of associated fastq file:
### Handling single and paired end data
```
channel.fromFilePairs( params.fastq, size: -1 )
```
will thus give `[file_id, [read_1_file, read_2_file]]` for paired-end data and `[file_id, [read_1_file]]` for single-end data
For process that have to deal with single
```
...
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
if (reads.size() == 2)
"""
fastp --thread ${task.cpus} \
${params.fastp} \
--in1 ${reads[0]} \
--in2 ${reads[1]} \
--out1 ${file_prefix}_R1_trim.fastq.gz \
--out2 ${file_prefix}_R2_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
"""
else if (reads.size() == 1)
"""
fastp --thread ${task.cpus} \
${params.fastp} \
--in1 ${reads[0]} \
--out1 ${file_prefix}_trim.fastq.gz \
--html ${file_prefix}.html \
--json ${file_prefix}_fastp.json \
--report_title ${file_prefix}
"""
...
```
## `src/.docker_modules` guide lines
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