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feat: Add phylogenomics entries (#145)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| #!/usr/bin/env python | ||
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| # Input check for post-assembly "Phylogenomics" workflow | ||
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| import os | ||
| import sys | ||
| from samplesheet_utils import parse_args, make_dir, print_error | ||
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| def check_samplesheet(file_in, file_out): | ||
| """ | ||
| This function checks that the samplesheet follows the following structure: | ||
| sample,gff_file_path | ||
| sample,gff_file_path | ||
| """ | ||
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| sample_mapping_dict = {} | ||
| with open(file_in, "r") as fin: | ||
| ## Check header | ||
| MIN_COLS = 2 | ||
| HEADER = ["sample", "gff_file_path"] | ||
| header = [x.strip('"') for x in fin.readline().strip().split(",")] | ||
| if header[: len(HEADER)] != HEADER: | ||
| print( | ||
| "ERROR: Please check samplesheet header -> {} != {}".format( | ||
| ",".join(header), ",".join(HEADER) | ||
| ) | ||
| ) | ||
| sys.exit(1) | ||
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| ## Check sample entries | ||
| for line in fin: | ||
| lspl = [x.strip().strip('"') for x in line.strip().split(",")] | ||
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| # Check valid number of columns per row | ||
| if len(lspl) < len(HEADER): | ||
| print_error( | ||
| "Invalid number of columns (minimum = {})!".format(len(HEADER)), | ||
| "Line", | ||
| line, | ||
| ) | ||
| num_cols = len([x for x in lspl if x]) | ||
| if num_cols < MIN_COLS: | ||
| print_error( | ||
| "Invalid number of populated columns (minimum = {})!".format( | ||
| MIN_COLS | ||
| ), | ||
| "Line", | ||
| line, | ||
| ) | ||
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| ## Check sample name entries | ||
| sample, gff_file_path = lspl[: len(HEADER)] | ||
| if sample: | ||
| if sample.find(" ") != -1: | ||
| print_error("Sample entry contains spaces!", "Line", line) | ||
| else: | ||
| print_error("Sample entry has not been specified!", "Line", line) | ||
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| ## Check assembly gff file extension | ||
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| if gff_file_path: | ||
| if gff_file_path.find(" ") != -1: | ||
| print_error("gff file path contains spaces!", "Line", line) | ||
| if not gff_file_path.endswith(".gff") and not gff_file_path.endswith( | ||
| ".gff3" | ||
| ): | ||
| print_error( | ||
| "Phylo files must be one of .gff or .gff3.", | ||
| "Line", | ||
| line, | ||
| ) | ||
| """ | ||
| ## Auto-detect paired-end/single-end | ||
| sample_info = [] ## [single_end, fastq_1, fastq_2] | ||
| if sample and fastq_1 and fastq_2: ## Paired-end short reads | ||
| sample_info = ["0", fastq_1, fastq_2] | ||
| elif sample and fastq_1 and not fastq_2: ## Single-end short reads | ||
| sample_info = ["1", fastq_1, fastq_2] | ||
| else: | ||
| print_error("Invalid combination of columns provided!", "Line", line) | ||
| """ | ||
| sample_info = gff_file_path | ||
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| ## Create sample mapping dictionary = { sample: path } | ||
| if sample not in sample_mapping_dict: | ||
| sample_mapping_dict[sample] = sample_info | ||
| # TODO Come back to this conditional; does it make sense for multiple assemblies to one sample? | ||
| else: | ||
| if sample_info in sample_mapping_dict[sample]: | ||
| print_error("Samplesheet contains duplicate rows!", "Line", line) | ||
| else: | ||
| # sample_mapping_dict[sample].append(sample_info) | ||
| print_error( | ||
| "Mutliple files associated to one sample!", "Line", line | ||
| ) | ||
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| ## Write validated samplesheet with appropriate columns | ||
| if len(sample_mapping_dict) > 0: | ||
| out_dir = os.path.dirname(file_out) | ||
| make_dir(out_dir) | ||
| with open(file_out, "w") as fout: | ||
| fout.write(",".join(["sample", "path"]) + "\n") | ||
| for sample in sorted(sample_mapping_dict.keys()): | ||
| fout.write( | ||
| ",".join( | ||
| ["{}".format(sample), "{}".format(sample_mapping_dict[sample])] | ||
| ) | ||
| + "\n" | ||
| ) | ||
| else: | ||
| print_error("No entries to process!", "Samplesheet: {}".format(file_in)) | ||
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| def main(args=None): | ||
| args = parse_args(args) | ||
| check_samplesheet(args.FILE_IN, args.FILE_OUT) | ||
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| if __name__ == "__main__": | ||
| sys.exit(main()) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| import os | ||
| import sys | ||
| import errno | ||
| import argparse | ||
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| def parse_args(args=None): | ||
| Description = "Reformat nf-core/arete samplesheet file and check its contents." | ||
| Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>" | ||
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| parser = argparse.ArgumentParser(description=Description, epilog=Epilog) | ||
| parser.add_argument("FILE_IN", help="Input samplesheet file.") | ||
| parser.add_argument("FILE_OUT", help="Output file.") | ||
| return parser.parse_args(args) | ||
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| def make_dir(path): | ||
| if len(path) > 0: | ||
| try: | ||
| os.makedirs(path) | ||
| except OSError as exception: | ||
| if exception.errno != errno.EEXIST: | ||
| raise exception | ||
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| def print_error(error, context="Line", context_str=""): | ||
| error_str = "ERROR: Please check samplesheet -> {}".format(error) | ||
| if context != "" and context_str != "": | ||
| error_str = "ERROR: Please check samplesheet -> {}\n{}: '{}'".format( | ||
| error, context.strip(), context_str.strip() | ||
| ) | ||
| print(error_str) | ||
| sys.exit(1) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| include { PHYLOSHEET_CHECK } from '../../modules/local/samplesheet_check' | ||
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| // Input to the phylo work flow is different | ||
| // Instead of reads, pass in GFF files | ||
| workflow PHYLO_INPUT_CHECK { | ||
| take: | ||
| samplesheet | ||
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| main: | ||
| PHYLOSHEET_CHECK ( samplesheet ) | ||
| .splitCsv ( header:true, sep:',' ) | ||
| .map { get_sample_info_phylo(it) } | ||
| .set { genomes } | ||
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| //Check that no dots "." are in sample ID | ||
| genomes | ||
| .map { meta, reads -> meta.id } | ||
| .subscribe { if ( "$it".contains(".") ) exit 1, "Please review data input, sampleIDs may not contain dots, but \"$it\" does." } | ||
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| emit: | ||
| genomes // channel: [ val(meta), [ reads ] ] | ||
| } | ||
| // Function to get list of [ meta, [ path ] ] | ||
| def get_sample_info_phylo(LinkedHashMap row) { | ||
| def meta = [:] | ||
| meta.id = row.sample | ||
| meta.single_end = true | ||
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| def array = [] | ||
| if (!file(row.path).exists()) { | ||
| print("***") | ||
| print(row) | ||
| print("***") | ||
| exit 1, "ERROR: Please check input samplesheet -> Sequence file does not exist!\n${row.path}" | ||
| } | ||
| array = [ meta, file(row.path)] | ||
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| return array | ||
| } |
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