Giters

zavolanlab / PAQR_KAPAC

scripts, pipelines and documentation to run PAQR and KAPAC; KAPAC allows to infer regulatory sequence motifs implicated in 3’ end processing changes; PAQR enables the quantification of poly(A) site usage from standard RNA-seq data

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

snakemake symlink problem

aleighbrown opened this issue · comments

commented 
snakemake -s part_two.Snakefile -n -p
MissingInputException in line 42 of /SAN/vyplab/alb_projects/tools/PAQR_KAPAC/PAQR/part_two.Snakefile:
Missing input files for rule create_coverages:
test_study/valid_samples/wt_1.bam

Link 235 in the part_one.Snakefile creates a broken a symlink if config['dir.input"] is already a full path

bam_file = "../../" + config["dir.input"] + "/" + config[curr_uuid]['bam'] + ".bam"

The fix here was just removing the unnecessary "../../"

commented

Many thanks for the comment. You are right in the sense that we intended the program to run with relative path which is the cleaner way in our ways.

I included an additional sentence in the PAQR readme to stress this point.
Best
Ralf