Adding conditional in a snakemake wrapper shell section
This is a general question, not specific about the STAR wrapper
I faced today the issue that the STAR wrapper has a built in optional argument which users might want to change but cannot do by adding the modified option in the extra options because the STAR exe will complain about duplicate argument definition.
Is it possible to scan the extra options in a module and when a partial duplicate is found with a default options use the extra option string rather than the default
In my case the default in teh shell section is:
--outSAMtype BAM Unsorted
and my preferred (ideally added to the params list) is:
--outSAMtype BAM SortedByCoordinate
I would like the shell to run the params string instead of its default, making this wrapper more flexible
snakemake
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
add a comment |
This is a general question, not specific about the STAR wrapper
I faced today the issue that the STAR wrapper has a built in optional argument which users might want to change but cannot do by adding the modified option in the extra options because the STAR exe will complain about duplicate argument definition.
Is it possible to scan the extra options in a module and when a partial duplicate is found with a default options use the extra option string rather than the default
In my case the default in teh shell section is:
--outSAMtype BAM Unsorted
and my preferred (ideally added to the params list) is:
--outSAMtype BAM SortedByCoordinate
I would like the shell to run the params string instead of its default, making this wrapper more flexible
snakemake
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
add a comment |
This is a general question, not specific about the STAR wrapper
I faced today the issue that the STAR wrapper has a built in optional argument which users might want to change but cannot do by adding the modified option in the extra options because the STAR exe will complain about duplicate argument definition.
Is it possible to scan the extra options in a module and when a partial duplicate is found with a default options use the extra option string rather than the default
In my case the default in teh shell section is:
--outSAMtype BAM Unsorted
and my preferred (ideally added to the params list) is:
--outSAMtype BAM SortedByCoordinate
I would like the shell to run the params string instead of its default, making this wrapper more flexible
snakemake
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
This is a general question, not specific about the STAR wrapper
I faced today the issue that the STAR wrapper has a built in optional argument which users might want to change but cannot do by adding the modified option in the extra options because the STAR exe will complain about duplicate argument definition.
Is it possible to scan the extra options in a module and when a partial duplicate is found with a default options use the extra option string rather than the default
In my case the default in teh shell section is:
--outSAMtype BAM Unsorted
and my preferred (ideally added to the params list) is:
--outSAMtype BAM SortedByCoordinate
I would like the shell to run the params string instead of its default, making this wrapper more flexible
snakemake
snakemake
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
asked Nov 15 '18 at 9:09
splaisansplaisan
19712
19712
add a comment |
add a comment |
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