22 add polypolish tool (#49)

* add polypolish module * fixed multiqc * fixed workflow
fmalmeida · May 19, 2023 · d4b8977 · d4b8977
1 parent 8ea57fc
commit d4b8977
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Showing 6 changed files with 87 additions and 19 deletions.
diff --git a/environment.yml b/environment.yml
@@ -39,13 +39,16 @@ dependencies:
   - bioconda::nanopolish=0.13.2
   - bioconda::pbgcpp=2.0.2
   - bioconda::pbmm2=1.7.0
+  - bioconda::polypolish=0.5.0
   - bioconda::flye=2.9
   - bioconda::quast=5.2.0
   - bioconda::miniasm=0.3_r179
   - bioconda::seqtk=1.3
   - bioconda::shovill=1.1.0
   - bioconda::shasta=0.11
+  # - bioconda::trycycler=0.5.4
   - bioconda::haslr=0.8a1
+  # - biocconda::homopolish=0.4.1
   - bioconda::raven-assembler=1.6.1
   - bioconda::multiqc>=1.14
   - bioconda::csvtk=0.23.0

diff --git a/modules/Hybrid/polypolish.nf b/modules/Hybrid/polypolish.nf
diff --git a/modules/QualityAssessment/multiqc.nf b/modules/QualityAssessment/multiqc.nf
diff --git a/modules/QualityAssessment/quast.nf b/modules/QualityAssessment/quast.nf
diff --git a/workflows/assembly_qc.nf b/workflows/assembly_qc.nf
diff --git a/workflows/hybrid.nf b/workflows/hybrid.nf