rm demux_just_fwd_processing splitter_binary

Author: antgonza

src/sequence_processing_pipeline/Commands.py

@@ -252,6 +252,9 @@ def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
     dumb = iter(fp)
     qual = iter(fp)
 
+    # there is only fwd so the orientation is always '1'
+    orientation = '1'
+
     for i, s, d, q in zip(seq_id, seq, dumb, qual):
         # '@1', 'LH00444:84:227CNHLT4:7:1101:41955:2443/1'
         # '@1', 'LH00444:84:227CNHLT4:7:1101:41955:2443/1 BX:Z:TATGACACATGCGGCCCT' # noqa
@@ -267,25 +270,6 @@ def demux_just_fwd_processing(id_map, fp, out_d, task, maxtask):
 
         current_fp = openfps[fname_encoded]
 
-        # remove '\n' from sid and split on all whitespace.
-        tmp = sid.strip().split()
-
-        if len(tmp) == 1:
-            # sequence id line contains no optional metadata.
-            # don't change sid.
-            # -1 is \n
-            orientation = sid[-2]
-            sid = rec + sid
-        elif len(tmp) == 2:
-            sid = tmp[0]
-            metadata = tmp[1]
-            # no '\n'
-            orientation = sid[-1]
-            # hexdump confirms separator is ' ', not '\t'
-            sid = rec + sid + ' ' + metadata + '\n'
-        else:
-            raise ValueError(f"'{sid}' is not a recognized form")
-
         current_fp[orientation].write(sid)
         current_fp[orientation].write(s)
         current_fp[orientation].write(d)

src/sequence_processing_pipeline/templates/nuqc_job_single.sh

@@ -125,10 +125,6 @@ function mux-runner () {
     python {{pmls_path}} <(zcat ${jobd}/seqs.movi.txt.gz) {{pmls_extra_parameters}} | \
         seqtk subseq ${seq_reads_filter_alignment} - > ${jobd}/seqs.final.fastq
 
-    {{splitter_binary}} ${jobd}/seqs.final.fastq \
-        ${jobd}/reads.r1.fastq ${delimiter} ${r1_tag} &
-    wait
-
     # keep seqs.movi.txt and migrate it to NuQCJob directory.
     mv ${jobd}/seqs.movi.txt.gz {{output_path}}/logs/seqs.movi.${SLURM_ARRAY_TASK_ID}.txt.gz
 }
@@ -139,7 +135,7 @@ function demux-runner () {
     n_demux_jobs=${SLURM_CPUS_PER_TASK}
     jobd=${TMPDIR}
     id_map=${jobd}/id_map
-    seqs_r1=${jobd}/reads.r1.fastq.paired.fq
+    seqs_r1=${jobd}/seqs.final.fastq
 
     id_map=${jobd}/id_map
     if [[ ! -f ${id_map} ]]; then