[Do not merge!] Pseudo PR for first release#69
[Do not merge!] Pseudo PR for first release#69jfy133 wants to merge 1773 commits intofirst-commit-for-pseudo-prfrom
Conversation
jfy133
left a comment
jfy133
left a comment
There was a problem hiding this comment.
Overall looks pretty good, main things are:
- Add license to ALL scripts in
bin/(particularly for the package) - Make sure all version numbers are defined for all tools in the
condadeclaration of local modules with mulled containers,and these are exported.
workflows/circrna.nf
Outdated
| ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) | ||
| ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) | ||
| ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) | ||
| ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([])) |
There was a problem hiding this comment.
Is it correct only FastQC goes into MultiQC?
There was a problem hiding this comment.
I'll look into generating BAM stats
README.md
Outdated
| #   | ||
|
|
||
| **workflow for the quantification, differential expression analysis and miRNA target prediction analysis of circRNAs in RNA-Seq data**. | ||
| [](https://nf-co.re/circrna/results)[](https://doi.org/10.5281/zenodo.XXXXXXX) |
There was a problem hiding this comment.
README.md
Outdated
| 4. circRNA annotation | ||
| 5. Export mature spliced length as FASTA file | ||
| 6. Annotate parent gene, underlying transcripts. | ||
| 7. circRNA count matrix |
There was a problem hiding this comment.
Are these the custom R scripts? Otherwise maybe also link the tools here in a similar fashion to above
There was a problem hiding this comment.
Nope, vanilla python and bash.
| section_name: "nf-core/circrna Methods Description" | ||
| section_href: "https://github.com/nf-core/circrna" | ||
| plot_type: "html" | ||
| ## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline |
There was a problem hiding this comment.
you might want to add your paper here
There was a problem hiding this comment.
I'll give it a go! I went to the Sarek one to copy but... ;)
bin/ensembl_database_map.txt
Outdated
| @@ -0,0 +1,18 @@ | |||
| species command | |||
| cel useMart(biomart = "ensembl", dataset = "celegans_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) | |||
There was a problem hiding this comment.
This fetches the newest version every time, right? I am a bit worried about reproducibility and compatibility in the long run. Would there be a way to cache it?
There was a problem hiding this comment.
Think I'll deprecate this code, its only going to cause trouble
| } | ||
| } | ||
|
|
||
| // PREPARE GENOME |
There was a problem hiding this comment.
I suspect you will get WARN messages if the indices already exist
There was a problem hiding this comment.
I'll test this. I have a hard time resolving WARN messages
conf/modules.config
Outdated
|
|
||
| // PREPARE GENOME | ||
| withName: BOWTIE_BUILD { | ||
| ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } |
There was a problem hiding this comment.
what happens if params.tools doesn't exist? Or does it always have to have a value?
There was a problem hiding this comment.
must have a value, a la --tool 'mutect2', --step 'mapping' ..
conf/test_full.config
Outdated
| // Input data for full size test | ||
| // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) | ||
| // TODO nf-core: Give any required params for the test so that command line flags are not needed | ||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' |
There was a problem hiding this comment.
nope, I was hoping for some help in getting my full test dataset up and running.
| @@ -1,63 +1,590 @@ | |||
| # nf-core/circrna: Output | |||
|
|
|||
| ## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/circrna/output](https://nf-co.re/circrna/output) | |||
There was a problem hiding this comment.
is this line removed in the template @jfy133 ?
Important! Template update for nf-core/tools v3.2.0
Update modules
|
@FriederikeHanssen , @nictru , just checking this is work in progress? |
|
The story of this pipeline is a bit unsatisfying: This PR is still open from the time before I took over development. Actually I did not dare to close it, not sure what the official thing to do is in this situation. |
|
Ok, then I will close it and you can start the release when you are ready. Thanks! |
9 participants
Do not merge! This is a PR of dev compared to first release for whole-pipeline reviewing purposes.
Comments can be copied over to #66 for safety if necessary and changes made there. Changes should be made to
devand this PR should not be merged intofirst-commit-for-pseudo-pr!