Commit c11c58c0 authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

updated summary of bins

parent 6896d29c
......@@ -46,6 +46,11 @@ outputs:
doc: GTDB-Tk output directory
type: Directory?
outputSource: gtdbtk_files_to_folder/results
bins_summary:
label: Bins summary
doc: Summary of info about the bins
type: File
outputSource: bins_summary/bins_summary
inputs:
identifier:
......@@ -150,14 +155,17 @@ steps:
out: [binDepths]
#############################################
#### Bin assembly statistics
bins_stats:
doc: Table of all bins and their assembly statistics like N50
label: Bin assembly stats
run: ../metagenomics/bin_assembly_stats.cwl
bins_summary:
doc: Table of all bins and their statistics like size, contigs, completeness etc
label: Bins summary
run: ../metagenomics/bins_summary.cwl
in:
identifier: identifier
bin_dir: metabat2/bin_dir
out: [binStats,binContigs]
busco_dir: busco_files_to_folder/results
bin_depths: aggregate_bin_depths/binDepths
checkm: checkm/checkm_out_table
out: [bins_summary, bin_contigs]
#############################################
#### Get unbinned contigs fasta
# workflow_getunbinned:
......@@ -170,15 +178,15 @@ steps:
# assembly_fasta: assembly
# bin_dir: workflow_metabat2/bin_dir
# out: [unbinned_fasta]
#############################################
#### General bin and assembly read mapping stats
############################################
### General bin and assembly read mapping stats
bin_readstats:
doc: Table general bin and assembly read mapping stats
label: Bin and assembly read stats
run: ../metagenomics/assembly_bins_readstats.cwl
in:
identifier: identifier
binContigs: bins_stats/binContigs
binContigs: bins_summary/bin_contigs
idxstats: contig_read_counts/contigReadCounts
flagstat: assembly_read_counts/flagstat
out: [binReadStats]
......@@ -275,8 +283,8 @@ steps:
label: MetaBat2 output folder
run: ../expressions/files_to_folder.cwl
in:
files:
source: [metabat2/log, bins_stats/binStats, bin_readstats/binReadStats, bins_stats/binContigs, metabat2_contig_depths/depths, aggregate_bin_depths/binDepths]
files:
source: [metabat2/log, bins_summary/bin_contigs ,bin_readstats/binReadStats, metabat2_contig_depths/depths, aggregate_bin_depths/binDepths]
linkMerge: merge_flattened
folders:
source: [metabat2/bin_dir]
......
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