Merge pull request #107 from nf-core/pranathivemuri-patch-2

update sencha version

CHANGELOG.md

@@ -19,6 +19,7 @@ Initial release of nf-core/kmermaid, created with the [nf-core](http://nf-co.re/
 * Add samtools_fastq_unaligned and samtools_fastq_aligned process for converting bam to per cell
 barcode fastq
 * Add version printing for sencha, bam2fasta, and sourmash in Dockerfile, update versions in environment.yml
+* For processes translate, sourmash compute  add cpus=1 as they are only serial ([#107](https://github.com/nf-core/kmermaid/pull/107))
 
 ### `Fixed`
 
@@ -33,6 +34,7 @@ barcode fastq
 * Used `.combine()` instead of `each` to do cartesian product of all possible molecules, ksizes, and sketch values
 * Use ripgrep instead of bam2fasta to make per-cell fastq, which will hopefully make resuming long-running pipelines on bams much faster
 * Fix the use of `skip_multiqc` flag condition with if and not when
+* Updated sencha=1.0.3 to fix the bug in memory errors possibly with the numpy array on unique filenames ([PR #96 on sencha](https://github.com/czbiohub/leaftea/pull/96))
 
 ### `Dependencies`
 

conf/base.config

@@ -58,7 +58,16 @@ process {
     memory = { check_max( 2.GB * task.attempt, 'memory' ) }
     cache = false
   }
-
+  withName: 'sourmash_compute_sketch_fastx_nucleotide|sourmash_compute_sketch_fastx_peptide' {
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+    time = { check_max( 96.h * task.attempt, 'time' ) }
+    cpus = { check_max (1, 'cpus')}
+  }
+  withName: 'translate' {
+    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+    time = { check_max( 96.h * task.attempt, 'time' ) }
+    cpus = { check_max (1, 'cpus')}
+  }
   withLabel: mid_cpu {
     memory = { check_max( 16.GB * task.attempt, 'memory') }
     cpus = { check_max( 8 * task.attempt, 'cpus' ) }

environment.yml

@@ -38,4 +38,4 @@ dependencies:
   - ripgrep=12.1.1
   - pip:
     - bam2fasta==1.0.8
-    - sencha==1.0.2
+    - sencha==1.0.3