Update bakta, write tmp data to local work dir (#33)

* Update bakta, write tmp data to local work dir * Update nextflow.config
BCCDC-PHL · Sep 30, 2022 · 630f0a1 · 630f0a1
1 parent f0c6450
commit 630f0a1
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Showing 4 changed files with 20 additions and 16 deletions.
diff --git a/environments/bakta.yml b/environments/bakta.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bakta=1.2.1
+  - bakta=1.5.1
diff --git a/main.nf b/main.nf
@@ -4,21 +4,21 @@ import java.time.LocalDateTime
 
 nextflow.enable.dsl = 2
 
-include { hash_files } from './modules/hash_files.nf'
-include { fastp } from './modules/fastp.nf'
-include { fastp_json_to_csv } from './modules/fastp.nf'
-include { filtlong } from './modules/long_read_qc.nf'
-include { nanoq as nanoq_pre_filter } from './modules/long_read_qc.nf'
+include { hash_files }                 from './modules/hash_files.nf'
+include { fastp }                      from './modules/fastp.nf'
+include { fastp_json_to_csv }          from './modules/fastp.nf'
+include { filtlong }                   from './modules/long_read_qc.nf'
+include { nanoq as nanoq_pre_filter }  from './modules/long_read_qc.nf'
 include { nanoq as nanoq_post_filter } from './modules/long_read_qc.nf'
-include { merge_nanoq_reports } from './modules/long_read_qc.nf'
-include { unicycler } from './modules/unicycler.nf'
-include { prokka } from './modules/prokka.nf'
-include { bakta } from './modules/bakta.nf'
-include { quast } from './modules/quast.nf'
-include { parse_quast_report } from './modules/quast.nf'
-include { bandage } from './modules/long_read_qc.nf'
-include { pipeline_provenance } from './modules/provenance.nf'
-include { collect_provenance } from './modules/provenance.nf'
+include { merge_nanoq_reports }        from './modules/long_read_qc.nf'
+include { unicycler }                  from './modules/unicycler.nf'
+include { prokka }                     from './modules/prokka.nf'
+include { bakta }                      from './modules/bakta.nf'
+include { quast }                      from './modules/quast.nf'
+include { parse_quast_report }         from './modules/quast.nf'
+include { bandage }                    from './modules/long_read_qc.nf'
+include { pipeline_provenance }        from './modules/provenance.nf'
+include { collect_provenance }         from './modules/provenance.nf'
 
 
 workflow {

diff --git a/modules/bakta.nf b/modules/bakta.nf
@@ -28,8 +28,12 @@ process bakta {
       printf -- "        - parameter: --keep-contig-headers\\n"                >> ${sample_id}_${assembler}_${assembly_mode}_bakta_provenance.yml
       printf -- "          value: null\\n"                                     >> ${sample_id}_${assembler}_${assembly_mode}_bakta_provenance.yml
 
+      mkdir tmp
+
       bakta \
         --threads ${task.cpus} \
+        --tmp-dir ./tmp \
+        --debug \
         --db ${params.bakta_db} \
         --compliant \
         --keep-contig-headers \

diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/routine-assembly'
-  version = '0.4.0'
+  version = '0.4.1'
   description = 'BCCDC-PHL Routine Assembly'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'