--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nf/subworkflows/ncbi/shared/diamond/main.nf	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,107 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+
+/*
+ *Execution of: 
+ * /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/bin/diamond 
+ *    -asn-cache /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/sequence_cache 
+ *    -blastp-args '--sam-query-len --comp-based-stats 0 --evalue 0.0001 --very-sensitive --max-hsps 3' 
+ *    -diamond-executable /netmnt/vast01/gpi/regr/GPIPE_REGR1/system/2024-03-27.prod.build25780/third-party/diamond/diamond 
+ *    -lds2 /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/prot_gnomon_prepare.8202002/out/LDS2 
+ *    -ofmt seq-align-set 
+ *    -output-dir /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out 
+ *    -output-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/out/align.mft 
+ *    -output-prefix hits 
+ *    ## query is gnomon-made proteins 'gnl|GNOMON|23016146.p'
+ *    ## query-fmt is <String, `fasta', `seq-ids'>
+ *    -query-fmt seq-ids 
+ *    -query-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/query_ids.mft 
+ *    ## subject is swiss-prot ids 'sp|A0A009IHW8.1|ABTIR_ACIB9'
+ *    -subject-fmt seq-ids 
+ *    -subject-manifest /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/inp/subject_ids.mft 
+ *    -work-area /netmnt/vast01/gpi/regr/GPIPE_REGR1/data00/Gavia_stellata/GP37025.85624/846757/diamond.8202022/tmp
+
+ */
+
+include {to_map; shellSplit } from '../../utilities'
+
+
+swiss_prot_url='https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/reference_sets/swissprot.asnb.gz'
+process fetch_swiss_prot_asn  {
+    input:
+    output:
+        path "output/swissprot.asnb", emit: "swiss_prot_asn"
+    script:
+    """
+        curl -O '$swiss_prot_url'
+        gunzip swissprot.asnb.gz
+        mkdir -p output
+        mv swissprot.asnb output/swissprot.asnb
+    """   
+    stub:
+    """
+        mkdir -p output
+        touch output/swissprot.asnb
+    """
+}
+
+process get_swiss_prot_ids {
+    input:
+        path swiss_prot_asn
+    output:
+        path "output/swiss_prot_ids"
+    script: 
+    """
+        mkdir -p output
+        lds2_indexer  -db lds -source  .
+        sqlite3 ./lds "SELECT txt_id FROM seq_id WHERE orig=1 AND int_id IS NULL;"    > output/swiss_prot_ids
+    """
+    stub:
+    """
+        mkdir -p output
+        touch output/swiss_prot_ids
+    """
+}
+
+process run_diamond_egap {
+    input:
+        path gnomon_prot_ids
+        path swiss_prot_ids
+        path gnomon_prot_asn, stageAs: 'indexed/*'
+        path swiss_prot_asn, stageAs: 'indexed/*'
+        val params
+    output:
+        path "output/*"
+    script:
+    // print(params)
+    """
+   
+    ###diamond_bin=`which diamond`
+    #diamond_egap uses GP_HOME to build paths to both some gp apps, and third-party
+    #GP_HOME needs to be the directory that contains third-party, and the directory that contains bin/<gp apps> 
+    diamond_bin=\${GP_HOME}/third-party/diamond/diamond
+    
+    mkdir -p ./asncache/
+
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${gnomon_prot_asn} -oseq-ids /dev/null -split-sequences
+    prime_cache -cache ./asncache/ -ifmt asnb-seq-entry  -i ${swiss_prot_asn} -oseq-ids /dev/null -split-sequences
+
+    mkdir ./output
+    mkdir ./work
+
+    echo  ${params}
+    echo "${gnomon_prot_ids.join('\n')}" > query.mft
+    diamond_egap  ${params} -asn-cache ./asncache/ -nogenbank -query-manifest query.mft -subject ${swiss_prot_ids} \
+        -output-dir ./output/ -work-area ./work/  -diamond-executable \${diamond_bin}
+    rm -rf ./work
+    """
+
+    stub:
+    """
+    mkdir -p output
+    touch output/diamond_output.asn
+    """
+}
+
+