Final checks pre 0.3.4 release

open2c · Nov 10, 2022 · 0b8ffca · 0b8ffca
1 parent 074170e
commit 0b8ffca
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Showing 3 changed files with 7,152 additions and 3,239 deletions.
diff --git a/distiller.nf b/distiller.nf
@@ -139,7 +139,7 @@ def fastqDumpCmd(file_or_srr, library, run, srr_start=0, srr_end=-1, threads=1,
     if (use_custom_split) {
         cmd = """
             #cp -r $HOME/.ncbi/ . # Fix for sra-tools requiring ncbi folder locally
-            HOME=`readlink -e ./`
+            #HOME=`readlink -e ./`
             fastq-dump ${file_or_srr} -Z --split-spot ${srr_start_flag} ${srr_end_flag} \
                         | pyfilesplit --lines 4 \
                             >(bgzip -c -@{bgzip_threads} > ${library}.${run}.1.fastq.gz) \
@@ -150,7 +150,7 @@ def fastqDumpCmd(file_or_srr, library, run, srr_start=0, srr_end=-1, threads=1,
     } else {
         cmd = """
             #cp -r $HOME/.ncbi/ .  # Fix for sra-tools requiring ncbi folder locally
-            HOME=`readlink -e ./`
+            #HOME=`readlink -e ./`
             fastq-dump ${file_or_srr} --gzip --split-spot --split-3 ${srr_start_flag} ${srr_end_flag} 
             mv *_1.fastq.gz ${library}.${run}.1.fastq.gz
             mv *_2.fastq.gz ${library}.${run}.2.fastq.gz