Same as issue #6

[jloubser]

Good day,
I get this error when trying to run the pipeline on the example fastqs (I get the same error on my own fastqs as well):

"(transflow) [jloubser@khaos transflow]$ bash transflow.sh --configfile config/configfile.yaml --cores 4
1st step: Generate quality control statistics (based on fastqc and MultiQC) ...
[*] Parsing all samples from the metadata file.

=> Total number of samples: 10

=> Samples are:

['S1', 'S2', 'S3', 'S4', 'S5', 'S6', 'S7', 'S8', 'S9', 'S10']
Wildcard constraints in inputs are ignored. (rule: clip)
Building DAG of jobs...
InputFunctionException in rule merge_reads in file /home/jloubser/transflow/workflow/rules/transition.smk, line 24:
Error:
NameError: name 'subprocess' is not defined
Wildcards:
smp=S1
Traceback:
File "/home/jloubser/transflow/workflow/rules/transition.smk", line 38, in
File "/home/jloubser/transflow/workflow/quality_control.snakefile", line 73, in read_length_from_name
File "/home/jloubser/transflow/workflow/quality_control.snakefile", line 63, in read_length_from_file
2nd step: variants calling (based on MTB pan-genome & bwa + GATK3) ...
FileNotFoundError in file /home/jloubser/transflow/workflow/variant_calling.snakefile, line 19:
[Errno 2] No such file or directory: '2.MTBC_identification/MTBC_samples.txt'
File "/home/jloubser/transflow/workflow/variant_calling.snakefile", line 19, in
3rd step: sample clustering and transmission events predicting (based on transcluster + SeqTrack) ...
FileNotFoundError in file /home/jloubser/transflow/workflow/transmission_analysis.snakefile, line 13:
[Errno 2] No such file or directory: '2.MTBC_identification/MTBC_samples.txt'
File "/home/jloubser/transflow/workflow/transmission_analysis.snakefile", line 13, in
4th step: generating a summary report (html format)..."

[jloubser]

Additionally, when trying to run it step by step using snakemake I get this error:

(transflow) [jloubser@khaos workflow]$ snakemake quality_control.snakefile --configfile ../config/configfile.yaml --cores 4
Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.

[jloubser]

Could it be that the pipeline can't even access the snakemake files since it does not recognize it or am I missing something obvious?
I tried tinkering a bit with the .yaml file and specifying specific versions of Python for example but no luck.

[jloubser]

I get the same errors when trying to run the pipeline on our server as well as on an Ubuntu machine (wsl subsystem). So it doesnt appear to be system specific.