From df4842dd05352559a4bce005dc833dcf85237e71 Mon Sep 17 00:00:00 2001 From: MokaGuys Date: Thu, 19 Oct 2023 12:05:49 +0100 Subject: [PATCH] update samplesheet splitting function and correct error in for loop for post run commands list for TSO --- upload_and_setoff_workflows.py | 60 +++++++++++++++++++++++----------- 1 file changed, 41 insertions(+), 19 deletions(-) diff --git a/upload_and_setoff_workflows.py b/upload_and_setoff_workflows.py index 027670d3..d110dba1 100644 --- a/upload_and_setoff_workflows.py +++ b/upload_and_setoff_workflows.py @@ -647,14 +647,36 @@ def split_TSO500_samplesheet(self): # samplesheet in the runfolder samplesheet_file = os.path.join(self.runfolder_obj.runfolderpath, self.runfolder_obj.runfolder_samplesheet_name) + samplesheet_header = [] + samples = [] + no_sample_lines = 0 + expected_data_headers = ["Sample_ID", "Sample_Name", "index"] + # Read all lines from the sample sheet with open(samplesheet_file) as samplesheet: - all_lines = samplesheet.readlines() + for line in reversed(samplesheet.readlines()): + # stop when get to data headers section + if any(header in line for header in expected_data_headers): + break + # skip empty lines (check first element of the line, after splitting on comma) + elif len(line.split(",")[0]) < 2: + pass + # If its a line containing a sample:: + elif line.startswith("TSO"): + samples.append(line) + no_sample_lines += 1 + # get header + with open(samplesheet_file) as samplesheet: + for line in samplesheet.readlines(): + # stop when get to data headers section- add header line to header then break + if any(header in line for header in expected_data_headers): + samplesheet_header.append(line) + break + else: + samplesheet_header.append(line) - # Separate header from samples. TSO samplesheet header is the first 25 lines of the file - samplesheet_header = all_lines[:25] - # sample lines start with "TSO". This excludes empty lines below the samples list, i.e. lines containing ",,,,,,," - samples = [sample for sample in all_lines[25:] if sample.startswith("TSO")] + # reverse samples list to get back in correct order (starting at sample 1) + samples.reverse() # Split samples into batches (size specified in config) # batches is a list of lists, where each list is a subset of the samples from the samplesheet @@ -1676,23 +1698,23 @@ def build_TSO500_post_run_commands(self): TSOcommands_list.append( self.create_fastqc_command(sample) ) - # Only add to depends_list if job ID from previous command - # is not empty - TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list(sample, 'depends_list')) - - TSOcommands_list.append(self.create_sambamba_cmd(sample, pannumber)) - # Exclude negative controls from the depends list as the NTC - # coverage calculation can often fail. We want the coverage - # report for the NTC sample to help assess contamination. - # Only add to depends_list if job ID from previous command - # is not empty - TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list(sample, 'depends_list')) + # Only add to depends_list if job ID from previous command + # is not empty + TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list(sample, 'depends_list')) - if "HD200" in sample: - TSOcommands_list.append(self.create_sompy_cmd(sample, pannumber)) + TSOcommands_list.append(self.create_sambamba_cmd(sample, pannumber)) + # Exclude negative controls from the depends list as the NTC + # coverage calculation can often fail. We want the coverage + # report for the NTC sample to help assess contamination. # Only add to depends_list if job ID from previous command # is not empty - TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list("sompy", 'depends_list')) + TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list(sample, 'depends_list')) + + if "HD200" in sample: + TSOcommands_list.append(self.create_sompy_cmd(sample, pannumber)) + # Only add to depends_list if job ID from previous command + # is not empty + TSOcommands_list.append(self.if_jobid_exists_depends % self.add_to_depends_list("sompy", 'depends_list')) TSOcommands_list.append(self.create_upload_multiqc_command(TSO500)) TSOcommands_list.append(self.add_to_depends_list("UploadMultiQC", 'depends_list'))