pipeline does not work if fastp rule is deactivate

sequana / rnaseq

RNA-seq, QC and differential analysis pipeline

BSD 3-Clause "New" or "Revised" License

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pipeline does not work if fastp rule is deactivate #15

Closed ddesvillechabrol closed 1 year ago

ddesvillechabrol commented 2 years ago

#######################################################
# sofware__choice = ["atropos", "cutadapt", "fastp"]
trimming:
    software_choice: fastp
    do: false

MissingInputException in line 351 of /pasteur/zeus/projets/p02/Biomics/Bioinfo/InProgress/B6766/analysis/rnaseq/rnaseq.rules:
Missing input files for rule sample_rRNA:
D080322_N_CD4_TCR_100_S2/fastp/D080322_N_CD4_TCR_100_S2_R1_.fastp.fastq.gz

cokelaer commented 1 year ago

Indeed, syntax error and issues with other trimming tools such as cutadapt and atropos. All fixed in future PR https://github.com/sequana/rnaseq/pull/31