Code

Dev store downsample data#94

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chrisgulvik merged 215 commits intodevbacterial-genomics/wf-paired-end-illumina-assembly:devfrom dev-store-downsample-databacterial-genomics/wf-paired-end-illumina-assembly:dev-store-downsample-dataCopy head branch name to clipboardNov 15, 2024

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Commits

Commits on Aug 25, 2024

• save more stats, logs, and intermediate FastQ files prior to final cleaned reads

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• save subsampled FastQ only for seqtk; save cleaned FastQ for hostile

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Commits on Aug 26, 2024

• hostile files stored without dirname and .clean_[12] name that hostile adds to it

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• add process_medium to RDP Classifier to avoid wasted first run fail due to not enough memory (RAM)

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• store intermediate Fastp output FastQ files as well

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Commits on Aug 27, 2024

• migrated from greg to staph-b for container -- staph-b now has v1.4 with tests

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• migrate to v1.4 docker container now that staph-b has it with tests

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• rename Fastp summary filename

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• save system call stdout stderr logfiles for all of the missing modules

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• add default seed to downsampling and hide new seed parameters by default

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• add parameter option for subsample_tool to include seqkit as well as default seqtk

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• edit summary TSV handling, which now creates XLSX

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• use collectFile() for CheckM2 TSV Summary file; commented out previous one-liner that tried to do this

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• add SeqKit as subsampling option; add toLower() function

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• fix shell comparison if ${pplacer_scratch} path is set and not empty

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• add params.config with default seed value for seqkit

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• add new module for subsampling FastQ reads with SeqKit

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• set default seed value for seqtk

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• create default params.seqtk_seed set to 947266746; print with msg the seed value used for R1 and R2; cleanup comments

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• add --create_excel_outputs to the UGE runner script

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• use locally stored CheckM2 database in the runner script

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• fixed missing brackets

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Commits on Aug 28, 2024

• revise blastn output file to use underscores instead of spaces in header column names

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• revise Quast TSV output file to use underscores instead of spaces in header line only

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• revise CheckM2.report.tsv output file to use underscores instead of spaces in the header line

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• bugfix: change spaces to underscores in the CheckM2.report.tsv

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• replace spaces with underscores in header of .FLASH.tsv files

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• replace spaces with lines in TSV header output of AlignmentStats

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• add feature that reports stdev beside the mean depth of coverage values (sum of squares math in awk!)

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• replaced spaces with underscored in header of CleanedReads-Bases.tsv output file

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• replace spaces with underscores in header file of .fastp.tsv output file

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• replace spaces with underscores in header of .Trimmomatic.tsv output file

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• replace spaces with underscores in header of output file

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• replace spaces with underscores in header line of .kraken_summary.tsv output files; also fix issue with missing column header names in the .kraken_summary.tsv output files

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• replace spaces with underscores in header line of .kraken2_summary.tsv output files; also fix issue with missing column header names in the .kraken_summary.tsv output files

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• replace spaces with underscores in header line of phix output summary files

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• replace spaces with underscores in headers

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• replaced spaces with underscores in header line

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• replaced spaces with underscores in header lines

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• replaced spaces with underscores in header line output file

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• fix \\t tab issues; replace spaces with underscores in header output files

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• replaced spaces with underscores in header output files

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• replaced spaces with tabs in header of output files

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• replaced spaces with underscores in header column names of output TSV files

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• replaced spaces with underscores in header column names in output tsv files

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• replaced spaces with underscores in header column names for output TSV files

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• replaced spaces with underscores in header column names of output TSV files

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• replace spaces with underscores in header column names of output TSV files

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• replace all spaces with underscores in header column names of output TSV files

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• replace all spaces with underscores in header column names in TSV output files

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• replace spaces with underscores in header output TSV file

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• bugfix attempt with additional "error_bad_lines=False" option during pandas read_csv function

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• bugfix attempt: print offending TSV filenames but try to complete conversion with good ones; also store pandas version

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• bugfix attempt handling XLSX pandas issue with different columns in data than header due to spaces (e.g., "Neural Network (Specific Model)")

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• bugfix with awk not using tab "awk -F '\t'" --> "awk -F $'\t'"

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• added subsample_tool,seqtk_seed,seqkit_seed; excluded all MLST databases by default with a *_<int> such as leptospira_2 and leptospira_3

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• remove commented bash cmds as example backup parsing due to runtime error

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• Update CHANGELOG.md for v2.4.0

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• [MegaLinter] Apply linters fixes

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• Exclude all MLST databases by default with a *_<int> such as leptospira_2 and leptospira_3

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• change MLST output format to exclude file extension, clarify assembler name in header, replace spaces with underscores in header column names

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• remove trailing tab present in Kraken2 data output TSV that's absent in Kraken1 data output

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• fixed trailing tab character in Kraken1 and Kraken2 output TSV summaries, which made pandas XLSX conversion fail due to different column numbers in header and data

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• skip tab replacement, now handled in the bin/summarize_kraken.sh function for both Kraken1 and Kraken2

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• edit RDP module to ensure consistent output TSV column number with fixrank default option

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• replace sed with awk commands in MLST output summaries to avoid shell compatibility issues

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Commits on Sep 3, 2024

• update to make XLSX with color-coating tabs work for Summary-Report

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• changed CheckM2 report and Summary-Report.xlsx output filenames

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• changed !{meta.id}.CheckM2.report.tsv into !{meta.id}-!{meta.assembler}.CheckM2.results.tsv output reports

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• fixed VERSION reporting RDP bug by removing spaces; added more verbose messaging before and after RDP system call

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• append assembler name to MLST results to avoid misinterpretation of mixed assembler outputs

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• add assembler name to output filenames

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• remove % symbol from data cells in report, and remove trailing tab in header line

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• more verbose messaging and commented warning too little RAM

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• remove % symbol from data cells in report, and remove trailing tab in header line

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• added seqfu but cannot use due to filesize M suffix not interpreted due to different find version than GNU Ubuntu

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• avoid overwriting the input file; changed output filename; removed trailing tab in header line; removed % character from data cells

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• added stdev depth metrics; added total paired+single mapped stats; revised header column names

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• report stdev depths in Summary file if present; actually use calculations now to fallback on tallies if mapped files are absent or problematic; change nextflow variables to clarify content of each

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• changed Summary TSV filenames

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• changed code throughout to get XLSX creation working for Kraken, Kraken2, 16S RDP, 16S BLAST, and MLST; added lots of debug printing statements of files going in and out of channels throughout

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• [MegaLinter] Apply linters fixes

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Commits on Sep 4, 2024

• change msg ERROR to stderr not stdout

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• add SHA-256 checksums to input FastQ files

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Commits on Sep 5, 2024

• added saving of checksum files

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• changed 16S BLASTn QC file header to clarify TSV format

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• changed assembly QC file header to clarify FastA format

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• changed assembly QC file header to clarify FastA format

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• changed header output to unify Sample_name as first column; changed assembly filename in data row to simply the meta.id (sample name)

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• shorten outfile wrangling commands

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• split Sample_name and Integer counter 16S rRNA into separate data columns (and header); simplify outfile wrangling

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• updated colors and tab names

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• removed assembler name from MLST data output to unify reporting of just Sample_name meta.id

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• added Sample_name meta.id into data column

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• revised headers on QC files to clarify FastA and BAM formats

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• revised outfile to exclude assembler name and unify Sample_name meta.id reporting style

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• changed INFO messages to stdout not stderr; added checksum of CleanedReads; clarified file formats in QC files

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• revised QC header to clarify BAM file format tested

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• changed QC header files to clarify FastQ and FastA file formats tested

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• removed commented lines no longer useful

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• bugfix to now allow CheckM2 summaries to be put into XLSX Summary-Report; sort file content based on Sample_name

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• added FastQ format validation test; added checksum reporting; sort file content by Sample_name

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• minor style edit

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• added FastQ format validation test

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Commits on Sep 6, 2024

• exclude assembler var name in output QC file

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• added checksum calculations

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• bugfix added header line to QC CheckM2 file

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• edit colors

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• discard assembler name from QC outfile

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• added checksum calcs; discarded assembler varname from QC outfiles

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• bugfix add header line to QC outfiles

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• added checksums

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• added checksums

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Commits on Sep 7, 2024

• made script executable with git update-index --chmod=+x script.sh

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Commits on Sep 17, 2024

• sorted publication list based on software name; added publication citations to software used (e.g., CheckM2, CAT, Fastp

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• updated description on output files based on new files created as well as some renamed output files

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• sorted based on section titles for easier tracking; added many additional output files to be saved

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• removed option to save discarded contig stats and FastA output; that is now default always on

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• updated Prokka container from snads to staph-b

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• updated container from greg to staph-b

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• updated SPAdes to v4.0 from greg to staph-b

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• changed RDP output to exclude unneccesary data columns such as "Phylum\nphylum", "Genus\ngenus"

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• use both R1 and R2 and only Phred30 for estimate bp input for more accurate estimation of genome size

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• added colors to additional tabs in XLSX summarized

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• updated container from snads to staph-b

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• changed default to always on to store stats and FastA of discarded contigs during biopython filtering

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• removed option (default is always on now) to store discarded contigs FastA file

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• revised to only use quality and sequence strings for checksums

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• left commented out but begin checksum eval of Kraken1 database input

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• left commented out but begin checksum eval of Kraken2 database input

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• updated mlst container from greg to staph-b which includes a more updated MLST database; add messaging throughout to improve debugging

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• update container from snads to staph-b; change summary report from .FLASH.tsv to Overlap.tsv; only use quality and sequence for checksums

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• add Sample_name info for all correction outputs to unify reporting style

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• no longer use cleaned_fastq_files for QA Assembly QUAST process; fix global to single sed replacement; quast syscall no longer modifies stdout/stderr messages; update container from snads to staph-b

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• add information during messaging throughout to help debugging; remove stderr/stdout messaging during kraken-report syscall

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• add information during messaging throughout to help debugging

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• update container from snads to staph-b

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• add --force to hostile syscalls for overwriting; shorten QC File reporting; add checksums for host removal

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• changed bash variable to real arrays; avoid wildcards in outputs; added checksum for PhiX removal reads

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• increased CPU use for subsampling; fixed bug now create empty .Subsampled_FastQ.SHA256-checksums.tsv and versions.yml files when not downsampling; added checksums to reads

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• increased CPU use for subsampling; fixed bug now create empty .Subsampled_FastQ.SHA256-checksums.tsv and versions.yml files when not downsampling; added checksums to reads

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• changed INFO messages to go to stdout not stderr; changes QC File from .Adapter-removed_FastQ_File.tsv to more descriptive .Adapter_and_QC_Trimmed_FastQ_File.tsv; added checksums of reads

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• bigfix on Trimmomatic order of filtering operations now <50 bp reads discarded; updated container from snads to staph-b; added checksums to reads

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• removed option (default is always ON now) to store contig stats and FastA discarded

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• stylistic updates

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• added ch_read_counts; removed sending ch_cleaned_fastq_files.join to the QA_ASSEMBLY_QUAST process; changed inputs for CALCULATE_COVERAGE_UNIX process to only ch_assembly_file and ch_read_alignment…

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• added CALC_STATS_DOWNSAMPLE_FQ_SEQTK and CALC_STATS_DOWNSAMPLE_FQ_SEQKIT to report sequence stats after downsampling; added ch_output_summary_filesto handle additional stats files being summarized

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• added CALC_STATS_HOST_REMOVED_FQ_SEQKIT to report sequence stats after host removal; added ch_output_summary_files to ensure all sequence stats are Summary.<file>.tsv summarized

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• added CALC_STATS_INPUT_FQ_SEQKIT, CALC_STATS_NOPHIX_FQ_SEQKIT, CALC_STATS_TRIM_FQ_SEQKIT, CALC_STATS_CLEANEDREADS_FQ_SEQKIT to report sequence stats after PhiX removal and QC trimming steps (each);…

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• new modules that report additional metrics on the FastQ files; used often for metrics reporting after a read cleaning step (e.g., mean, smallest, largest read sizes, total bp and reads, etc.)

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• add SeqKit option to estimate input Phred30+ R1 and R2 sequences for genome size estimation; no longer rely on Seqtk when specifying SeqKit for downsampling even for its metrics reporting here

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Commits on Sep 20, 2024

• changed Trimmomatic output summary format; from 256 to 512 sum

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• changed Fastp output summary format; from 256 to 512 sum

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• expand db file structure of SRA Human Scrubber example

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• changed from 256 to 512 sum

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• changed from 256 to 512 sum

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• added progress messaging; changed SRA Scrubber output summary header information; changed SRA Scrubber output summary filename; added 512 checksum reporting

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• changed Hostile removal output summary filename; added more progress messaging; from 256 to 512 sum

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• changed BBTools Repair removal output summary content and filename; added 512 checksum

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• stylistic changes in ordering

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• removed gene calling from QUAST output summary because so few are going to have up-to-date ~/.gm_key anyways; added progress messaging

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• upgraded Kraken2 software version from greg to Staph-B

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• upgraded Kraken1 software version from greg to Staph-B

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• added progress messaging; from 256 to 512 sum

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• changed min_filesize_binary_pe_alignment from 25M to 6M to allow for 10x of about 2.5 Mbp genome

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• changed min_filesize_binary_pe_alignment from 25M to 6M to allow for 10x of about 2.5 Mbp genome; updated output filenames

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• changed min_filesize_binary_pe_alignment from 25M to 6M to allow for 10x of about 2.5 Mbp genome; removed gtdbtk_min_perc_aa and gtdbtk_pplacer_cpus variables due to upgraded GTDB-Tk classification…

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• upgraded GTDB-Tk from v2.3.2 to v2.4.0

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• nf-core modules logged during software version upgrade

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• changed the date format to show month by name (MMM) and also include day of the week (EEE)

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• no longer use 2 channels for Assembly_Assessment; shortened Summary TSV filenames to help pandas XLSX conversion

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• added extra progress messaging; from 256 to 512 sum

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• decreased min_filesize_binary_pe_alignment from 25MB to 6MB

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• changed RDP container now that Staph-B pulled Taylor's Dockerfile

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• from 256 to 512 sum

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  95230dd

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• added extra progress messaging

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  3d306fe

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• changed output summary filename

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  2df5f94

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• from 256 to 512 sum

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  85b3b6a

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• from 256 to 512 sum

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  6d48a42

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• changed summary output filename

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• added GTDB-Tk classify tests

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• from 256 to 512

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• changed tab names based on updated filename outputs

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• updated default SRA Human Scrubber database from 2023 to 22024 version; removed 2 GTDB-Tk variables no longer used in updated nf-core module: gtdbtk_min_af gtdbtk_min_perc_aa

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• added shell quoting

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• reorganized output directory structure and handled renamed output files

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Commits on Oct 7, 2024

• added category, title, and subject options

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• added header for QC outfile

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• switched to Staph-B supported container

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• store novel FastA when that situation occurs

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• discard extra args related to gene finding

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• added wf version to XLSX outfile

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• increase process to high due to bottleneck

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• added colors for nondefault processes such as CheckM2, BUSCO, and GTDB-Tk

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• added output path and additional debug messages throughout

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• revised bash comparison due to nf-core bug

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• added metrics and checksums to each host remove step

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• revised output statement when <= 0x depth given

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• revised QC Trim output filename; added wf version number to XLSX summary outfile

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• revise input requirements; changed BUSCO, CheckM2, and GTDB-Tk processes

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• revise input requirements; changed BUSCO, CheckM2, and GTDB-Tk processes

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  1191201

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• changed mash_db default because GTDB-Tk doesnt use external, only locally built one so it isnt necessary

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• shortened withName: statements; revised output dir structure for Assembly/QA and Taxonomy/

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• changed date format for output files; added additional bash variable quoting

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• [MegaLinter] Apply linters fixes

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Commits on Oct 11, 2024

• bugfix reporting number 16S seqeuences now extracts last item in underscore delimited string

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• bugfix reporting number 16S seqeuences now extracts last item in underscore delimited string

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• Merge branch 'dev-store-downsample-data' of github.com:bacterial-genomics/wf-paired-end-illumina-assembly into dev-store-downsample-data

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Commits on Nov 15, 2024

• updated nf-core modules by uncommenting

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• changed default from seqtk to seqkit for downsampling

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  23c3854

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• discard old DAG image

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  3243803

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• updated wf process diagram

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• version bump

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• prettier changes

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• [MegaLinter] Apply linters fixes

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