change arg name

workflows/index-generation/index-generation.wdl

@@ -676,7 +676,7 @@ task SplitFastaBySeqLengthAndSort {
         total_seqs=$(grep ">" ~{fasta} | wc -l)
         ncbi-compress  break-up-fasta-by-sequence-length  \
             --input-fasta ~{fasta}  \
-            --temp-file-output-dir outputs  \
+            --output-dir outputs  \
             --total-sequence-count ${total_seqs}  \
             --bin-size 25 \
 

workflows/index-generation/ncbi-compress/src/commands.rs

@@ -1,8 +1,6 @@
 pub mod commands {
     use std::fs;
-    use std::fs::File;
-    use std::io::{self, BufRead};
-    use std::path::Path;
+    //use std::io::{self, BufRead};
 
     use tempdir::TempDir;
     use bio::io::fasta;
@@ -78,7 +76,7 @@ pub mod commands {
         let mut seq_count = 0;
         let mut split_count = 1;
         let mut writer = fasta::Writer::to_file(format!("{}/{}_{}.fa", output_dir, taxid, split_count)).unwrap();
-        for (i, record) in records_iter.enumerate() {
+        for (_i, record) in records_iter.enumerate() {
             let record = record.unwrap();
             writer.write_record(&record).unwrap();
             seq_count += 1;
@@ -113,13 +111,13 @@ pub mod commands {
         let mut accession_count = 0;
         let mut unique_accession_count = 0;
         let mut writer = fasta::Writer::to_file(output_fasta_path).unwrap();
-        for (i, entry) in fs::read_dir(input_taxid_dir).unwrap().enumerate() {
+        for (_i, entry) in fs::read_dir(input_taxid_dir).unwrap().enumerate() {
             let entry = entry.unwrap();
             let path = entry.path();
             let input_fasta_path = path.to_str().unwrap();
             let taxid = path.file_name().unwrap().to_str().unwrap().split(".").collect::<Vec<&str>>()[0];
             let reads_count = count_fasta_reads(input_fasta_path);
-            if reads_count >= 5 { //9500000 { // back of the envelope calculation for how many 50,000 character reads that we can store in 488GB of RAM 
+            if reads_count >= 9500000 { // back of the envelope calculation for how many 50,000 character reads we can store in 488GB of RAM 
                 log::info!("Breaking apart taxid {} into smaller chunks", taxid);
                 let input_taxid_dir = format!("{}/{}_split", input_taxid_dir, taxid);
                 split_fasta_into_chunks(&input_fasta_path, &input_taxid_dir, &reads_count, &3, taxid).expect("error splitting fasta into chunks");
@@ -130,7 +128,7 @@ pub mod commands {
                     Err(e) => println!("Error deleting input fasta : {:?}", e),
                 }
                 // recursively call fasta_compress_from_taxid_dir on the new directory containing the smaller chunks
-                for (i, entry) in fs::read_dir(input_taxid_dir).unwrap().enumerate() {
+                for (_i, entry) in fs::read_dir(input_taxid_dir).unwrap().enumerate() {
                     let entry = entry.unwrap();
                     let path = entry.path();
                     let split_taxid_fasta_path = path.to_str().unwrap();
@@ -241,7 +239,7 @@ pub mod commands {
         let mut accession_count = 0;
         let mut unique_accession_count = 0;
         let mut writer = fasta::Writer::to_file(output_fasta_path).unwrap();
-        for (i, entry) in fs::read_dir(taxid_dir).unwrap().enumerate() {
+        for (_i, entry) in fs::read_dir(taxid_dir).unwrap().enumerate() {
             let entry = entry.unwrap();
             let path = entry.path();
             let input_fasta_path = path.to_str().unwrap();

workflows/index-generation/ncbi-compress/src/logging.rs

@@ -48,9 +48,7 @@ pub mod logging {
             Ok(()) => {
                 println!("File removed successfully.");
             }
-            Err(e) => {
-                println!("Error while removing file: {}", e);
-            }
+            Err(e) => {} // logging file doesn't exist so we don't need to remove it
         };
 
         let file = OpenOptions::new()

workflows/index-generation/ncbi-compress/src/ncbi_compress.rs

@@ -68,7 +68,7 @@ pub mod ncbi_compress {
                 .from_path(mapping_file_path)
                 .unwrap();
             let mut added = 0;
-            reader.into_records().enumerate().for_each(|(i, result)| {
+            reader.into_records().enumerate().for_each(|(_i, result)| {
                 // if i % 10_000 == 0 {
                 //     log::info!("  Processed {} mappings, added {}", i, added);
                 // }
@@ -246,8 +246,6 @@ pub mod ncbi_compress {
                 }
             }
             for (hash, accession_id) in tmp {
-                // only insert accession_id into tree if logging is enabled
-
                 tree.insert(hash, accession_id).unwrap();
             }
             chunk = records_iter