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nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
https://nf-co.re/circdna
MIT License
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make --input_format a required argument when running local command line #65

Closed jluebeck closed 9 months ago

jluebeck commented 10 months ago

Description of feature

I ran nextflow run nf-core/circdna -r dev --input colo320dm_samplesheet.csv --outdir colo320dmlc_nftest --genome GRCh38 -profile docker --circle_identifier ampliconarchitect --mosek_license_dir $HOME/mosek --aa_data_repo $AA_DATA_REPO --reference_build GRCh38 --fasta $AA_DATA_REPO/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa

on my local machine, however the module assumed by default an --input_format FASTQ when my samplesheet.csv was 

sample,bam
COLO320DM_LC,/home/jens/Desktop/research/bams/COLO320DM_Hung2021.bam

and the pipeline crashed in a way that wasn't exactly clear why until I re-visited the web-form and saw that --input_format was a required field on the web form. Can we update so that --input_format is either required on the command-line or deduced from the samplesheet?

Thanks! Jens

DSchreyer commented 9 months ago

Thanks for reporting! Yeah, I agree. I will include that in v1.1