Is it possible to have more than one dynamic wildcard in my snakemake pipeline?
I have a working snakemake pipeline with a dynamic wildcard. However, when I try to add new rules that use a new/different dynamic wildcard, then everything stops working.
My question is: Can I have more than one dynamic wildcard in my pipeline?
Here is my general workflow
- Bin metagenomic reads into species clusters
- Using protein fasta of each bin/species, generate a genome scale model for each bin (this takes one dynamic wildcard)
- Using the DNA fasta of each bin/species generate an abundance and classification report for each bin (this takes another wildcard)
My second question is: Is there another approach besides using dynamic() that will satisfy my requirements? Or do I absolutely need to use dynamic()?
I can post my rules/code if it will help answer my question.
Thanks in advance.
python dynamic wildcard snakemake
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
add a comment |
I have a working snakemake pipeline with a dynamic wildcard. However, when I try to add new rules that use a new/different dynamic wildcard, then everything stops working.
My question is: Can I have more than one dynamic wildcard in my pipeline?
Here is my general workflow
- Bin metagenomic reads into species clusters
- Using protein fasta of each bin/species, generate a genome scale model for each bin (this takes one dynamic wildcard)
- Using the DNA fasta of each bin/species generate an abundance and classification report for each bin (this takes another wildcard)
My second question is: Is there another approach besides using dynamic() that will satisfy my requirements? Or do I absolutely need to use dynamic()?
I can post my rules/code if it will help answer my question.
Thanks in advance.
python dynamic wildcard snakemake
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33
add a comment |
I have a working snakemake pipeline with a dynamic wildcard. However, when I try to add new rules that use a new/different dynamic wildcard, then everything stops working.
My question is: Can I have more than one dynamic wildcard in my pipeline?
Here is my general workflow
- Bin metagenomic reads into species clusters
- Using protein fasta of each bin/species, generate a genome scale model for each bin (this takes one dynamic wildcard)
- Using the DNA fasta of each bin/species generate an abundance and classification report for each bin (this takes another wildcard)
My second question is: Is there another approach besides using dynamic() that will satisfy my requirements? Or do I absolutely need to use dynamic()?
I can post my rules/code if it will help answer my question.
Thanks in advance.
python dynamic wildcard snakemake
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
I have a working snakemake pipeline with a dynamic wildcard. However, when I try to add new rules that use a new/different dynamic wildcard, then everything stops working.
My question is: Can I have more than one dynamic wildcard in my pipeline?
Here is my general workflow
- Bin metagenomic reads into species clusters
- Using protein fasta of each bin/species, generate a genome scale model for each bin (this takes one dynamic wildcard)
- Using the DNA fasta of each bin/species generate an abundance and classification report for each bin (this takes another wildcard)
My second question is: Is there another approach besides using dynamic() that will satisfy my requirements? Or do I absolutely need to use dynamic()?
I can post my rules/code if it will help answer my question.
Thanks in advance.
python dynamic wildcard snakemake
python dynamic wildcard snakemake
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
asked Nov 14 '18 at 13:49
Francisco ZorrillaFrancisco Zorrilla
84
84
Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33
add a comment |
Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33
Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33
Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33
add a comment |
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Edit: I have made my pipeline work using two dynamic wildcards. It would still be nice to know if anyone has other approaches that circumvent the use of dynamic wildcards.
– Francisco Zorrilla
Nov 20 '18 at 13:33