Gensub inside a shell command in Snakemake

Question

# md5sum on fastq folder on cluster
rule md5sum_fastq_cluster:
     input:
         path_cluster+'/'+project_name+'/'+project_name+'.csv'
     output:
         path_cluster+'/'+project_name+'/'+'md5sum.txt'
     shell:
         """find {path_cluster}/{project_name} -type f -name "*.fastq.gz" -exec md5sum {{}} + | awk '{{print $1, gensub( ".*/", "", $2 )}}' | sort > {output}"""
 
 
 # md5sum on fastq folder on remote server
 rule md5sum_fastq_SAN:
     input:
         copyFASTQdone
     output:
         SFTPsan.remote(server_san+path_san+'/'+project_name+'/md5sum.txt')
     shell:
         """ssh imrb@{server_san} "find {path_san}/{project_name} -type f -name '*.fastq.gz' -exec md5sum {{}} + | awk '{{print \$1, gensub( ".*/", "", \$2 )}}' | sort" > {output}"""

--------------------------------------------------------------------------
awk: ligne de commande:1: {print $1, gensub( .*/, , $2 )}
awk: ligne de commande:1:                    ^ syntax error
awk: ligne de commande:1: {print $1, gensub( .*/, , $2 )}

Obviously my syntax for gensub is wrong
Before adding the gensub command, my 2 shell commands from the 2 rules were :

"""find {path_cluster}/{project_name} -type f -name "*.fastq.gz" -exec md5sum {{}} + | awk '{{print $1}}' | sort > {output}"""

"""ssh imrb@{server_san} "find {path_san}/{project_name} -type f -name '*.fastq.gz' -exec md5sum {{}} + | awk '{{print \$1}}' | sort > {output}"""

It was working. It's just since I added the gensub, I can't find the right syntax.
I need this gensub to basically do the same thing as basename to remove the path of my files.
And of course, I tried the awk/gensub command outside my snakemake, it works.

Just in case, here are the files produced by my rules :

# md5sum.txt before gensub
01afd3f2bf06d18c5609b2c2c963eddf /data/imrb/Data/200122_GSC/14-CTRL50TMZ1907192_S11_R2_001.fastq.gz
03e353c316aef09c748aa2363db95599 /data/imrb/Data/200122_GSC/15-11650TMZ1907192_S12_R2_001.fastq.gz
1ba21b8be882bcb62c464ba515800ca4 /data/imrb/Data/200122_GSC/1-CTRL120719_S1_R2_001.fastq.gz

# md5sum.txt after gensub
01afd3f2bf06d18c5609b2c2c963eddf 14-CTRL50TMZ1907192_S11_R2_001.fastq.gz
03e353c316aef09c748aa2363db95599 15-11650TMZ1907192_S12_R2_001.fastq.gz
1ba21b8be882bcb62c464ba515800ca4 1-CTRL120719_S1_R2_001.fastq.gz

Answer 1

Thanks to dariober I found the right syntax for each rule.

For the first rule : I need to escape the double quotes I use inside my awk

rule md5sum_fastq_cluster:
     input:
         path_cluster+'/'+project_name+'/'+project_name+'.csv'
     output:
         path_cluster+'/'+project_name+'/'+'md5sum.txt'
     shell:
         """find {path_cluster}/{project_name} -type f -name "*.fastq.gz" -exec md5sum {{}} + | awk '{{print $1, gensub( \".*/\", \"\", $2 )}}' | sort > {output}"""

For the second rule, the shell command is passed to SSH, I need to double escape my double quotes and add a \ before $2

 rule md5sum_fastq_SAN:
     input:
         copyFASTQdone
     output:
         SFTPsan.remote(server_san+path_san+'/'+project_name+'/md5sum.txt')
     shell:
         """ssh imrb@{server_san} "find {path_san}/{project_name} -type f -name '*.fastq.gz' -exec md5sum {{}} + | awk '{{print \$1, gensub( \\".*/\\", \\"\\", \$2 )}}' | sort" > {output}"""