# HG changeset patch
# User rliterman
# Date 1733346127 18000
# Node ID b6ec322b1f054e345214069d08862fe7b8b36b56
# Parent 893a6993efe34a464d71d8ad8f62f64678af9477
"planemo upload"
diff -r 893a6993efe3 -r b6ec322b1f05 CSP2/subworkflows/fetchData/main.nf
--- a/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 13:48:13 2024 -0500
+++ b/CSP2/subworkflows/fetchData/main.nf Wed Dec 04 16:02:07 2024 -0500
@@ -20,8 +20,7 @@
userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py")
// Set SKESA cores to 4 or fewer
-//skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
-skesa_cpus = 1
+skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
workflow {
main:
diff -r 893a6993efe3 -r b6ec322b1f05 csp2_screen.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/csp2_screen.xml Wed Dec 04 16:02:07 2024 -0500
@@ -0,0 +1,134 @@
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+ Screen query assemblies against reference assemblies
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+ nextflow
+ micromamba
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+ nextflow -version
+ Nextflow_Log.txt 2>&1;
+sleep 1;
+ ]]>
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+ This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
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+ 10.XXXX/placeholder.doi
+ @article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
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diff -r 893a6993efe3 -r b6ec322b1f05 csp2_snp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/csp2_snp.xml Wed Dec 04 16:02:07 2024 -0500
@@ -0,0 +1,157 @@
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+ Run SNP Pipeline analysis on isolates using one or more references.
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+ nextflow
+ micromamba
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+ nextflow -version
+ Nextflow_Log.txt 2>&1;
+sleep 1;
+ ]]>
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+ This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
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+ 10.XXXX/placeholder.doi
+ @article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
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diff -r 893a6993efe3 -r b6ec322b1f05 csp_screen.xml
--- a/csp_screen.xml Wed Dec 04 13:48:13 2024 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
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- Screen query assemblies against reference assemblies
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- nextflow
- micromamba
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- nextflow -version
- Nextflow_Log.txt 2>&1;
- sleep 5;
- zip -r work.zip work;
- zip -r csp2.zip CSP2_Screen_Output;
- ]]>
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- This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
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- 10.XXXX/placeholder.doi
- @article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
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