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Files in channels (follow best practices) #113

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Dec 17, 2018
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Files in channels (follow best practices) #113

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36c0acb
Channels CHANGELOG
apeltzer Dec 15, 2018
07e7ec6
Use channels !
apeltzer Dec 15, 2018
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

## [Unpublished / Dev Branch]

### `Added`
* [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow.

### `Fixed`
* [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)

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17 changes: 9 additions & 8 deletions main.nf
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Expand Up @@ -211,9 +211,10 @@ params.bamutils_softclip = false



multiqc_config = file(params.multiqc_config)
output_docs = file("$baseDir/docs/output.md")
wherearemyfiles = file("$baseDir/assets/where_are_my_files.txt")
ch_multiqc_config = Channel.fromPath(params.multiqc_config)
ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
Channel.fromPath("$baseDir/assets/where_are_my_files.txt")
.into{ ch_where_for_bwa_index; ch_where_for_fasta_index; ch_where_for_seqdict}

// Validate inputs
Channel.fromPath("${params.fasta}")
Expand Down Expand Up @@ -390,7 +391,7 @@ process makeBWAIndex {

input:
file fasta from ch_fasta_for_bwa_indexing
file wherearemyfiles
file wherearemyfiles from ch_where_for_bwa_index

output:
file "*.{amb,ann,bwt,pac,sa,fasta,fa}" into (ch_bwa_index,ch_bwa_index_bwamem)
Expand All @@ -417,7 +418,7 @@ process makeFastaIndex {

input:
file fasta from ch_fasta_for_faidx_indexing
file wherearemyfiles
file wherearemyfiles from ch_where_for_fasta_index

output:
file "${fasta}.fai" into ch_fasta_faidx_index
Expand Down Expand Up @@ -447,7 +448,7 @@ process makeSeqDict {

input:
file fasta from ch_fasta_for_dict_indexing
file wherearemyfiles
file wherearemyfiles from ch_where_for_seqdict

output:
file "*.dict" into ch_seq_dict
Expand Down Expand Up @@ -1009,7 +1010,7 @@ process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'

input:
file multiqc_config
file multiqc_config from ch_multiqc_config.collect().ifEmpty([])
file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([])
file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
file ('software_versions/*') from software_versions_yaml.collect().ifEmpty([])
Expand Down Expand Up @@ -1045,7 +1046,7 @@ process output_documentation {
publishDir "${params.outdir}/Documentation", mode: 'copy'

input:
file output_docs
file output_docs from ch_output_docs

output:
file "results_description.html"
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