samtools view: failed to open "batch10_20230518/results/encode5_batch11.5074_IP2_CLIP.umi.r1.fq.genome-mapped.bam" for reading: No such file or directory

[byee4]

Pipeline throws an error whenever samples come from different folders. Likely the result of the error in logic on this line:

https://github.com/YeoLab/eclip-qc/blob/b15edcb3f1127bec5ebd2b96807f4ab1b952fbb5/Snakefile#LL5C31-L5C31

Steps to reproduce: Use a yaml where two files from different directory sources are defined in SAMPLESPATH.

DB_N: "/projects/ps-yeolab3/bay001/annotations/nr/nt"
DB_X: "/projects/ps-yeolab3/bay001/annotations/nr/nr.dmnd"


N_downsample_reads: 25000

SAMPLESPATH:
  - /projects/ps-yeolab5/encode5/processing/ENCODE_batch10_20230518/results/encode5_batch10.5071_IP2_CLIP.umi.r1.fq.genome-mapped.bam
  - /projects/ps-yeolab5/encode5/processing/ENCODE_batch12_20230518/results/encode5_batch12.5072_IP1_CLIP.umi.r1.fq.genome-mapped.bam

output_folder: /home/bay001/projects/cst_encode5_20220624/permanent_data/debugger
SCRIPTS: /projects/ps-yeolab4/software/eclipdebugger/0.0.1/bin/eclip-qc/scripts/