Filename issue

[kcleal]

Hello,

I cant seem to get capcruncher to work with my data. This is my local folder:

CaC2_viewpoints.T2Tv2.17p.bed  DN10E19_S18_1.fastq.gz  DN9E1_S1_1.fastq.gz    DN9L14_S14_1.fastq.gz   HT29U12_S12_1.fastq.gz  PURO6E6_S6_2.fastq.gz  Undetermined_S0_1.fastq.gz
capcruncher_config.yml         DN10E19_S18_2.fastq.gz  DN9E1_S1_2.fastq.gz    DN9L14_S14_2.fastq.gz   HT29U12_S12_2.fastq.gz  PURO6E7_S7_1.fastq.gz  Undetermined_S0_2.fastq.gz
capcruncher_output             DN10E20_S19_1.fastq.gz  DN9E2_S2_1.fastq.gz    DN9L15_S15_1.fastq.gz   input_data.17p.tsv      PURO6E7_S7_2.fastq.gz
DN10E20_S19_2.fastq.gz  DN9E2_S2_2.fastq.gz    DN9L15_S15_2.fastq.gz   PURO6E4_S4_1.fastq.gz   PURO6E8_S8_1.fastq.gz
DN10E16_S16_1.fastq.gz         DN10L21_S20_1.fastq.gz  DN9E3_S3_1.fastq.gz    HT29U10_S10_1.fastq.gz  PURO6E4_S4_2.fastq.gz   PURO6E8_S8_2.fastq.gz
DN10E16_S16_2.fastq.gz         DN10L21_S20_2.fastq.gz  DN9E3_S3_2.fastq.gz    HT29U10_S10_2.fastq.gz  PURO6E5_S5_1.fastq.gz   PURO6E9_S9_1.fastq.gz
DN10E18_S17_1.fastq.gz         DN10L22_S21_1.fastq.gz  DN9L13_S13_1.fastq.gz  HT29U11_S11_1.fastq.gz  PURO6E5_S5_2.fastq.gz   PURO6E9_S9_2.fastq.gz
DN10E18_S17_2.fastq.gz         DN10L22_S21_2.fastq.gz  DN9L13_S13_2.fastq.gz  HT29U11_S11_2.fastq.gz  PURO6E6_S6_1.fastq.gz   run_capcruncher.sh

This is my input_data.17p.tsv file:

sample	condition
DN9E1_S1	Early
DN10E16_S16	Early
PURO6E4_S4	Early
HT29U10_S10	Early
DN9L13_S13	Late
DN10E20_S19	Late
PURO6E7_S7	Late

I run the pipeline like so:

capcruncher pipeline make --cores all

But I get this error:

/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/compare.smk:153: SyntaxWarning: invalid escape sequence '\.'
/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/compare.smk:185: SyntaxWarning: invalid escape sequence '\.'
/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/visualise.smk:78: SyntaxWarning: invalid escape sequence '\.'
  fig="capcruncher_output/results/figures/{viewpoint}.pdf",
/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/visualise.smk:79: SyntaxWarning: invalid escape sequence '\.'
  params:
/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/visualise.smk:138: SyntaxWarning: invalid escape sequence '\.'
/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/visualise.smk:139: SyntaxWarning: invalid escape sequence '\.'
Building DAG of jobs...
InputFunctionException in rule fastq_rename in file /home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/fastq.smk, line 148:
Error:
  KeyError: ' DN10E16_S16 _1.fastq.gz '
Wildcards:
  sample=DN10E16_S16
Traceback:
  File "/home/alex/miniconda3/lib/python3.12/site-packages/capcruncher/pipeline/workflow/rules/fastq.smk", line 150, in <lambda>

It looks like capcruncher is adding an extra space into the filename (see KeyError message). Ive experimented with adding spaces to the file name to try and get it to work, but to no avail. I have attached my config also.

Any ideas of what to try?

Thanks

capcruncher_config.zip