Open hoelzer opened 2 days ago
Ah I also removed your extra gzip FASTQ process bc I did not see why this is needed. Instead I do
samtools fastq ${bam_file} -T MM,ML | gzip -c - > ${sample_id}/${sample_id}.fastq.gz
and done. EDIT hm... but not sure if my way of directly piping the samtools output into gzip is super slow... o_O EDIT2 okay maybe it was also only slow bc I ran too much in parallel on my macbook
Test is currently running with my rndm example FASTA/BAM.
Please also do some test of this PR before merging. E.g. you can also test via
nextflow pull valegale/ONT_methylation
nextflow run valegale/ONT_methylation -r restructure ...
Hey @valegale I restructured your pipeline a bit to give you some guidance regarding:
--help
message that also shows default parametersI did not had perfect test data, so please expect maybe some bugs.
I tried my code using some rndm FASTA reference and a minimap2 sorted BAM I had around:
If you have multiple references and BAMs you would do:
and then, of course, their
.baseName
s have to match so that the channel is formed correctly.I also added a
--list
parameter, which allows you to provide CSV files as input. This might be handy because then you can do smt likewhere the content of these CSVs is smt like
I hope this restructuring also gives you some guidance how to easily add more processes, parameters, input options: if necessary.
Also, please feel free to rename parameters/channels if you think there are better alternatives.
If you are fine with the changes, please feel free to approve and merge this PR.