From 1d3ed88328f208909a420511bdf7021bef063b5d Mon Sep 17 00:00:00 2001
From: mult1fractal <stormrider935@googlemail.com>
Date: Thu, 11 Jan 2024 10:37:20 +0100
Subject: [PATCH] updated sourmash commands to sourmash 4.5 + fixed sourmash
 output file parsing

---
 configs/container.config                      |  2 +-
 .../sourmash_for_tax.nf                       |  2 +-
 workflows/process/sourmash/sourmash.nf        | 20 ++++++++++++++-----
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/configs/container.config b/configs/container.config
index 8c0367f..da22635 100644
--- a/configs/container.config
+++ b/configs/container.config
@@ -13,7 +13,7 @@ process {
     withLabel: python           { container = 'nanozoo/template:3.8--ccd0653' }
     withLabel: samtools         { container = 'nanozoo/samtools:1.9--76b9270' }
     withLabel: seqkit           { container = 'nanozoo/seqkit:0.13.2--cd66104' ; containerOptions = '--shm-size 2g' }
-    withLabel: sourmash         { container = 'nanozoo/sourmash:4.5.0--e12a57a'  }
+    withLabel: sourmash         { container = 'nanozoo/sourmash:4.5.0--e12a57a' }
     withLabel: ubuntu           { container = 'nanozoo/basics:1.0--962b907' }
     withLabel: upsetr           { container = 'nanozoo/upsetr:1.4.0--0ea25b3' }
     withLabel: vibrant          { container = 'multifractal/vibrant:0.5'  }
diff --git a/workflows/process/phage_tax_classification/sourmash_for_tax.nf b/workflows/process/phage_tax_classification/sourmash_for_tax.nf
index f34fc58..4263112 100644
--- a/workflows/process/phage_tax_classification/sourmash_for_tax.nf
+++ b/workflows/process/phage_tax_classification/sourmash_for_tax.nf
@@ -10,7 +10,7 @@ process sourmash_for_tax {
     shell:
       """
       for fastafile in ${fasta_dir}/*.fa; do
-        sourmash compute -p ${task.cpus} --scaled 100 -k 21 \${fastafile}
+        sourmash sketch dna -p k=21,scaled=100 \${fastafile}
       done
 
       for signature in *.sig; do
diff --git a/workflows/process/sourmash/sourmash.nf b/workflows/process/sourmash/sourmash.nf
index c466e0f..0266624 100644
--- a/workflows/process/sourmash/sourmash.nf
+++ b/workflows/process/sourmash/sourmash.nf
@@ -9,7 +9,7 @@ process sourmash {
     script:
         """
         for fastafile in ${fasta_dir}/*.fa; do
-          sourmash compute -p ${task.cpus} --scaled 100 -k 21 \${fastafile}
+          sourmash sketch dna -p k=21,scaled=100 \${fastafile}
         done
 
         for signature in *.sig; do
@@ -19,9 +19,9 @@ process sourmash {
         touch ${name}_\${PWD##*/}.list
 
         for tempfile in *.temporary; do
-          value=\$(grep -v "similarity,name,filename,md5" \${tempfile} | wc -l)   # filtering criteria
+          value=\$(grep -v "similarity,md5,filename,name,query_filename,query_name,query_md5,ani" \${tempfile} | wc -l)   # filtering criteria
           filename=\$(basename \${tempfile} .fa.sig.temporary)
-          prediction_value=\$(grep -v "similarity,name,filename,md5" \${tempfile} |sort -r -k1 | awk 'NR == 1' | cut -d "," -f1 )
+          prediction_value=\$(grep -v "similarity,md5,filename,name,query_filename,query_name,query_md5,ani" \${tempfile} |sort -r -k1 | awk 'NR == 1' | cut -d "," -f1 )
       
           if [ \$value -gt 0 ] 
             then echo "\$filename,\$prediction_value" >> ${name}_\${PWD##*/}.list
@@ -30,11 +30,21 @@ process sourmash {
         """
     stub:
         """
-        echo "similarity,name,filename,md5" > ${name}_\${PWD##*/}.list
+        echo "similarity,md5,filename,name,query_filename,query_name,query_md5,ani" > ${name}_\${PWD##*/}.list
         echo "pos_phage_1,1.0" >> ${name}_\${PWD##*/}.list
         """
 }
 
 /*
 filtering criteria is at line 24 (awk part) with a current similiarity of 0.5 or higher to known phages
-*/
\ No newline at end of file
+*/
+
+// for tempfile in *.temporary; do
+//           value=$(grep -v "similarity,name,filename,md5" ${tempfile} | wc -l)   # filtering criteria
+//           filename=$(basename ${tempfile} .fa.sig.temporary)
+//           prediction_value=\$(grep -v "similarity,name,filename,md5" \${tempfile} |sort -r -k1 | awk 'NR == 1' | cut -d "," -f1 )
+      
+//           if [ \$value -gt 0 ] 
+//             then echo "\$filename,\$prediction_value" >> ${name}_\${PWD##*/}.list
+//           fi
+//         done
\ No newline at end of file