Fix: Replace deblur commands with qiime2 plugin

segrelab · Nov 6, 2021 · 5f6a06c · 5f6a06c
1 parent 0a82089
commit 5f6a06c
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Showing 3 changed files with 24 additions and 27 deletions.
diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/deblur.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/deblur.nf
@@ -19,5 +19,6 @@ process deblur {
         ncpus = params.denoise_cluster.otu_assignment['deblur']['ncpus']
         min_reads = params.denoise_cluster.otu_assignment['deblur']['min_reads']
         min_size = params.denoise_cluster.otu_assignment['deblur']['min_size']
+        seq_type = params.paired_end ? "SampleData[PairedEndSequencesWithQuality]" : "SampleData[SequencesWithQuality]"
         template 'denoise_cluster/otu_assignment/deblur.sh'
 }
diff --git a/micone/pipelines/modules/denoise_cluster/otu_assignment/deblur_workflow.nf b/micone/pipelines/modules/denoise_cluster/otu_assignment/deblur_workflow.nf
@@ -8,15 +8,7 @@ workflow deblur_workflow {
         // tuple val(meta), file('trimmed/*.fastq.gz'), file('trimmed/MANIFEST'), file(sequence_metadata), file(samplemetadata_files)
         input_channel
     main:
-        if (params.paired_end) {
-            input_channel \
-                | join_reads \
-                | deblur
-        } else {
-            input_channel \
-                | deblur
-
-        }
+        deblur(input_channel)
         hashing3(
             deblur.out.meta_channel.first(),
             deblur.out.otu_channel.collect(),

diff --git a/micone/pipelines/templates/denoise_cluster/otu_assignment/deblur.sh b/micone/pipelines/templates/denoise_cluster/otu_assignment/deblur.sh
@@ -7,24 +7,28 @@ mv ${sequence_files} sequence_folder
 mv ${manifest_file} sequence_folder
 mv ${sequence_metadata} sequence_folder
 
-deblur workflow \
-    --seqs-fp  sequence_folder \
-    --output-dir deblur_output \
-    -t -1 \
-    --left-trim-length 0 \
-    --min-reads ${min_reads} \
-    --min-size ${min_size} \
-    --jobs-to-start ${ncpus} \
-    --keep-tmp-files
+qiime tools import \
+    --input-path sequence_folder \
+    --output-path seq_artifact.qza \
+    --type "${seq_type}"
 
-# Build otu table and rep seqs for the step before chimera checking
-mkdir otu_table
-deblur build-biom-table \
-    --min-reads ${min_reads} \
-    --file_type .trim.derep.no_artifacts.msa.deblur \
-    deblur_output/deblur_working_dir \
-    otu_table
+qiime deblur denoise-16S \
+    --i-demultiplexed-seqs seq_artifact.qza \
+    --p-trim-length -1 \
+    --p-min-reads ${min_reads} \
+    --p-min-size ${min_size} \
+    --p-jobs-to-start ${ncpus} \
+    --o-representative-sequences rep-seqs.qza \
+    --o-table table.qza \
 
-mv otu_table/all.biom ${meta.id}-${meta.run}_unhashed_otu_table.biom
-mv otu_table/all.seq.fa ${meta.id}-${meta.run}_unhashed_rep_seqs.fasta
+qiime tools export \
+    --input-path rep-seqs.qza \
+    --output-path rep_seqs
+
+qiime tools export \
+    --input-path table.qza \
+    --output-path table
+
+mv table/feature-table.biom ${meta.id}-${meta.run}_unhashed_otu_table.biom
+mv rep_seqs/dna-sequences.fasta ${meta.id}-${meta.run}_unhashed_rep_seqs.fasta
 mv ${samplemetadata_files} ${meta.id}-${meta.run}_sample_metadata.tsv