removed most legacy conditionals

microbiomedata · Jun 25, 2024 · aee52bf · aee52bf
1 parent 70c60cd
commit aee52bf
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Showing 5 changed files with 29 additions and 307 deletions.
diff --git a/annotation_full.wdl b/annotation_full.wdl
@@ -10,7 +10,7 @@ input {
   String  imgap_project_id
   String  database_location="/refdata/img/"
   String  imgap_project_type="metagenome"
-  String  gm_license="/refdata/licenses/.gmhmmp2_key"
+  String?  gm_license="/refdata/licenses/.gmhmmp2_key"
   Int     additional_threads=16
   String  container="microbiomedata/img-omics@sha256:d5f4306bf36a97d55a3710280b940b89d7d4aca76a343e75b0e250734bc82b71"
 
@@ -117,7 +117,6 @@ input {
        container=container,
        sa_execute = sa_execute,
        fa_execute = fa_execute,
-       map_execute = make_map_file.map_execute,
        map_info = make_map_file.out_log,
        structural_gff  = merge_outputs.structural_gff,
        imgap_version = split.imgap_version,
@@ -176,7 +175,6 @@ input {
       rfam_gff = merge_outputs.rfam_gff,
       product_names_tsv = merge_outputs.product_names_tsv,
       crt_crisprs = merge_outputs.crt_crisprs,
-      map_execute = make_map_file.map_execute,
       map_file = make_map_file.map_file,
       renamed_fasta = make_map_file.out_fasta
   }
@@ -212,8 +210,8 @@ input {
     File product_names_tsv = finish_ano.final_product_names_tsv
     File crt_crisprs = finish_ano.final_crt_crisprs
     File imgap_version = finish_ano.final_version
-    File? renamed_fasta = finish_ano.final_renamed_fasta
-    File? map_file = finish_ano.final_map_file
+    File renamed_fasta = finish_ano.final_renamed_fasta
+    File map_file = finish_ano.final_map_file
   }
 
   parameter_meta {
@@ -275,29 +273,21 @@ task make_map_file {
   }
 
   command <<<
-  find_prefix=`grep ~{proj_id} ~{input_file} | head -1`
-
-  set -euo pipefail
-  if [[ $find_prefix ]]
-  then
-    echo "false" > run_map.txt
-    ln ~{input_file} ~{prefix}_map.fasta || ln -s ~{input_file} ~{prefix}_map.fasta
-  else
-    echo "true" > run_map.txt
+    set -euo pipefail
+ 
     fasta_sanity.py -v
     fasta_sanity.py \
     -p ~{proj_id} \
     -l ~{min_seq_length} \
     -u ~{unknown_gap_length} \
     ~{input_file} ~{prefix}_map.fasta
-  fi
+
   >>>
 
   output{
-    File? map_file = "~{prefix}_contig_names_mapping.tsv"
+    File  map_file = "~{prefix}_contig_names_mapping.tsv"
     File  out_fasta = "~{prefix}_map.fasta"
     File  out_log = stdout()
-    Boolean map_execute = read_boolean("run_map.txt")
  }
   runtime {
     memory: "120G"
@@ -489,7 +479,6 @@ task make_info_file {
     input {
         String container
         String imgap_version
-        Boolean map_execute
         File map_info
         Boolean fa_execute
         Boolean sa_execute
@@ -522,12 +511,11 @@ task make_info_file {
     set -euo pipefail
      echo "IMGAP Version: ~{imgap_version}" > ~{prefix}_imgap.info
      #get map script version
-     if [[ "~{map_execute}" = true ]]
-       then
-       map_version=`grep "fasta_sanity.py" ~{map_info}`
-       map_version="Mapping Programs Used: $map_version"
-       echo $map_version >> ~{prefix}_imgap.info
-     fi
+
+     map_version=`grep "fasta_sanity.py" ~{map_info}`
+     map_version="Mapping Programs Used: $map_version"
+     echo $map_version >> ~{prefix}_imgap.info
+
      #get structual annotation versions
      if [[ "~{sa_execute}" = true ]]
        then
@@ -656,9 +644,8 @@ task finish_ano {
        File stats_json
        File product_names_tsv
        File crt_crisprs
-       Boolean map_execute
-       File? map_file
-       File? renamed_fasta
+       File map_file
+       File renamed_fasta
        String orig_prefix="scaffold"
        String sed="s/~{orig_prefix}_/~{proj}_/g"
     }
@@ -695,12 +682,9 @@ task finish_ano {
        cat ~{stats_json} | sed ~{sed} > ~{prefix}_stats.json
 
        ln ~{ano_info_file} ~{prefix}_imgap.info || ln -s ~{ano_info_file} ~{prefix}_imgap.info 
+       ln ~{map_file} ~{prefix}_contig_names_mapping.tsv || ln -s ~{map_file} ~{prefix}_contig_names_mapping.tsv
+       ln ~{renamed_fasta} ~{prefix}_contigs.fna || ln -s ~{renamed_fasta} ~{prefix}_contigs.fna
 
-       if [[ "~{map_execute}" = true ]]
-        then
-        ln ~{map_file} ~{prefix}_contig_names_mapping.tsv || ln -s ~{map_file} ~{prefix}_contig_names_mapping.tsv
-        ln ~{renamed_fasta} ~{prefix}_contigs.fna || ln -s ~{renamed_fasta} ~{prefix}_contigs.fna
-       fi
   >>>
 
    output {
@@ -731,8 +715,8 @@ task finish_ano {
         File final_product_names_tsv = "~{prefix}_product_names.tsv"
         File final_lineage_tsv = "~{prefix}_scaffold_lineage.tsv"
         File final_crt_crisprs = "~{prefix}_crt.crisprs"
-        File? final_renamed_fasta = "~{prefix}_contigs.fna"
-        File? final_map_file = "~{prefix}_contig_names_mapping.tsv"
+        File final_renamed_fasta = "~{prefix}_contigs.fna"
+        File final_map_file = "~{prefix}_contig_names_mapping.tsv"
         File final_tsv = "~{prefix}_stats.tsv"
         File final_version = "~{prefix}_imgap.info"
 

diff --git a/functional-annotation.wdl b/functional-annotation.wdl
@@ -6,31 +6,24 @@ workflow f_annotate {
         Int     additional_threads
        # File    input_contigs_fasta
         File    input_fasta
-        String  database_location
-        Boolean ko_ec_execute=true
+        String  database_location="/refdata/img/"
         String  ko_ec_img_nr_db="~{database_location}"+"/IMG-NR/20230629/img_nr"
         String  ko_ec_md5_mapping="~{database_location}"+"/IMG-NR/20230629/md5Hash2Data.tsv"
         String  ko_ec_taxon_to_phylo_mapping="~{database_location}"+"/IMG-NR/20230629/taxonOId2Taxonomy.tsv"
         String  lastal_bin="/opt/omics/bin/lastal"
         String  selector_bin="/opt/omics/bin/functional_annotation/lastal_img_nr_ko_ec_gene_phylo_hit_selector.py"
-        Boolean smart_execute=true
         Int?    par_hmm_inst
         Int?    approx_num_proteins
         String  smart_db="~{database_location}"+"/SMART/01_06_2016/SMART.hmm"
         String  hmmsearch_bin="/opt/omics/bin/hmmsearch"
         String  frag_hits_filter_bin="/opt/omics/bin/functional_annotation/hmmsearch_fragmented_hits_filter.py"
-        Boolean cog_execute=true
         String  cog_db="~{database_location}"+"/COG/HMMs/2003/COG.hmm"
-        Boolean tigrfam_execute=true
         String  tigrfam_db="~{database_location}"+"/TIGRFAM/v15.0/TIGRFAM.hmm"
         String  hit_selector_bin="/opt/omics/bin/functional_annotation/hmmsearch_hit_selector.py"
-        Boolean superfam_execute=true
         String  superfam_db="~{database_location}"+"/SuperFamily/v1.75/supfam.hmm"
-        Boolean pfam_execute=true
         String  pfam_db="~{database_location}"+"/Pfam/Pfam-A/v34.0/Pfam-A.v34.0.hmm"
         String  pfam_claninfo_tsv="~{database_location}"+"/Pfam/Pfam-A/v34.0/Pfam-A.clans.tsv"
         String  pfam_clan_filter="/opt/omics/bin/functional_annotation/pfam_clan_filter.py"
-        Boolean cath_funfam_execute=true
         String  cath_funfam_db="~{database_location}"+"/Cath-FunFam/v4.2.0/funfam.hmm"
         #  Boolean signalp_execute=true
         #  String  signalp_gram_stain="GRAM_STAIN"

diff --git a/prodigal.wdl b/prodigal.wdl