Fix: Add qiime2 DC module parameters

segrelab · Oct 19, 2021 · 91e0c51 · 91e0c51
1 parent 94231e0
commit 91e0c51
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Showing 7 changed files with 21 additions and 17 deletions.
diff --git a/micone/pipelines/configs/denoise_cluster.config b/micone/pipelines/configs/denoise_cluster.config
@@ -13,20 +13,21 @@ params {
             // Closed reference workflow
             'closed_reference' {
                 ncpus = 1
-                parameters = "${PWD}/nf_micone/data/qiime1_parameters.txt"
-                reference_sequences = "${PWD}/nf_micone/data/rep_set/97_otus.fasta"
+                percent_identity = 0.97
+                strand = "plus"
+                reference_sequences = "${PWD}/nf_micone/data/databases/greengenes/97/gg-ref-seqs.qza"
             }
             // Open reference workflow
             'open_reference' {
                 ncpus = 1
-                parameters = "${PWD}/nf_micone/data/qiime1_parameters.txt"
-                reference_sequences = "${PWD}/nf_micone/data/rep_set/97_otus.fasta"
-                picking_method = "uclust"
+                percent_identity = 0.97
+                strand = "plus"
+                reference_sequences = "${PWD}/nf_micone/data/databases/greengenes/97/gg-ref-seqs.qza"
             }
             // De novo workflow
             'de_novo' {
                 ncpus = 1
-                parameters = "${PWD}/nf_micone/data/qiime1_parameters.txt"
+                percent_identity = 0.97
             }
             // Dada2 workflow
             'dada2' {

diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/closed_reference.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/closed_reference.nf
@@ -13,9 +13,9 @@ process closed_reference {
     script:
         new_meta = updateMeta(meta)
         new_meta.denoise_cluster = 'closed_reference'
-        ncpus = params.denoise_cluster.otu_assignment['closed_reference']['ncpus']
-        parameters = params.denoise_cluster.otu_assignment['closed_reference']['parameters']
         reference_sequences = params.denoise_cluster.otu_assignment['closed_reference']['reference_sequences']
-        parallel_option = ncpus > 1 ? "-a -O ${ncpus}" : ''
+        percent_identity = params.denoise_cluster.otu_assignment['closed_reference']['percent_identity']
+        ncpus = params.denoise_cluster.otu_assignment['closed_reference']['ncpus']
+        strand = params.denoise_cluster.otu_assignment['closed_reference']['strand']
         template 'denoise_cluster/otu_assignment/pick_closed_reference_otus.sh'
 }
diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/de_novo.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/de_novo.nf
@@ -13,8 +13,7 @@ process de_novo {
     script:
         new_meta = updateMeta(meta)
         new_meta.denoise_cluster = 'de_novo'
+        percent_identity = params.denoise_cluster.otu_assignment['de_novo']['percent_identity']
         ncpus = params.denoise_cluster.otu_assignment['de_novo']['ncpus']
-        parameters = params.denoise_cluster.otu_assignment['de_novo']['parameters']
-        parallel_option = ncpus > 1 ? "-a -O ${ncpus}" : ''
         template 'denoise_cluster/otu_assignment/cluster_de_novo.sh'
 }
diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/open_reference.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/open_reference.nf
@@ -13,10 +13,9 @@ process open_reference {
     script:
         new_meta = updateMeta(meta)
         new_meta.denoise_cluster = 'open_reference'
-        ncpus = params.denoise_cluster.otu_assignment['open_reference']['ncpus']
-        parameters = params.denoise_cluster.otu_assignment['open_reference']['parameters']
         reference_sequences = params.denoise_cluster.otu_assignment['open_reference']['reference_sequences']
-        picking_method = params.denoise_cluster.otu_assignment['open_reference']['picking_method']
-        parallel_option = ncpus > 1 ? "-a -O ${ncpus}" : ''
+        percent_identity = params.denoise_cluster.otu_assignment['open_reference']['percent_identity']
+        strand = params.denoise_cluster.otu_assignment['open_reference']['strand']
+        ncpus = params.denoise_cluster.otu_assignment['open_reference']['ncpus']
         template 'denoise_cluster/otu_assignment/cluster_open_reference.sh'
 }
diff --git a/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_closed_reference.sh b/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_closed_reference.sh
@@ -13,8 +13,10 @@ qiime vsearch dereplicate-sequences \
 qiime vsearch cluster-features-closed-reference \
   --i-table table.qza \
   --i-sequences rep-seqs.qza \
-  --i-reference-sequences ${ref_seqs} \
+  --i-reference-sequences ${reference_sequences} \
   --p-perc-identity ${percent_identity} \
+  --p-strand ${strand} \
+  --p-threads ${ncpus} \
   --o-clustered-table table-cr.qza \
   --o-clustered-sequences rep-seqs-cr.qza \
   --o-unmatched-sequences unmatched-cr.qza

diff --git a/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_de_novo.sh b/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_de_novo.sh
@@ -14,6 +14,7 @@ qiime vsearch cluster-features-de-novo \
   --i-table table.qza \
   --i-sequences rep-seqs.qza \
   --p-perc-identity ${percent_identity} \
+  --p-threads ${ncpus} \
   --o-clustered-table table-dn.qza \
   --o-clustered-sequences rep-seqs-dn.qza
 

diff --git a/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_open_reference.sh b/micone/pipelines/templates/denoise_cluster/otu_assignment/cluster_open_reference.sh
@@ -13,8 +13,10 @@ qiime vsearch dereplicate-sequences \
 qiime vsearch cluster-features-open-reference \
   --i-table table.qza \
   --i-sequences rep-seqs.qza \
-  --i-reference-sequences ${ref_seqs} \
+  --i-reference-sequences ${reference_sequences} \
   --p-perc-identity ${percent_identity} \
+  --p-strand ${strand} \
+  --p-threads ${ncpus} \
   --o-clustered-table table-or.qza \
   --o-clustered-sequences rep-seqs-or.qza \
   --o-new-reference-sequences new-ref-seqs-or.qza