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Fix staging #44

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merged 2 commits into from
Jul 27, 2024
Merged

Fix staging #44

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d55822d
Fix staging
Jul 27, 2024
f60c480
Fix multiple map_file
Jul 27, 2024
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46 changes: 26 additions & 20 deletions mbin_nmdc.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@ workflow nmdc_mags {
supfam_file=supfam_file,
product_names_file=product_names_file,
gene_phylogeny_file=gene_phylogeny_file,
lineage_file=lineage_file
lineage_file=lineage_file,
map_file=map_file
}

call mbin_nmdc {
Expand All @@ -60,7 +61,7 @@ workflow nmdc_mags {
gtdbtk_env = gtdbtk_db,
checkm_env = checkm_db,
eukcc2_env = eukcc2_db,
map_file = map_file,
map_file = stage.map_tsv,
mbin_container = container
}
call package {
Expand Down Expand Up @@ -140,7 +141,7 @@ task mbin_nmdc {
Int? pthreads
String gtdbtk_env
String checkm_env
String? eukcc2_env
String? eukcc2_env
String mbin_container
}

Expand Down Expand Up @@ -192,7 +193,7 @@ task mbin_nmdc {
runtime{
docker : mbin_container
memory : "120 G"
time : "2:00:00"
time : "2:00:00"
cpu : threads
}

Expand All @@ -207,7 +208,7 @@ task mbin_nmdc {
File mbin_version = "mbin_nmdc_versions.log"
File bacsum = "gtdbtk-output/gtdbtk.bac120.summary.tsv"
File arcsum = "gtdbtk-output/gtdbtk.ar122.summary.tsv"
File eukcc_csv = "eukcc_output/eukcc.csv.final"
File eukcc_csv = "eukcc_output/eukcc.csv.final"
Array[File] hqmq_bin_fasta_files = glob("hqmq-metabat-bins/*fa")
Array[File] lq_bin_fasta_files = glob("filtered-metabat-bins/*fa")
}
Expand All @@ -232,6 +233,7 @@ task stage {
String product_names_file
String gene_phylogeny_file
String lineage_file
String? map_file
String contigs_out="contigs.fasta"
String bam_out="pairedMapped_sorted.bam"
String gff_out="functional_annotation.gff"
Expand All @@ -247,6 +249,7 @@ task stage {
String products_out="products.tsv"
String gene_phylogeny_out="gene_phylogeny.tsv"
String lineage_out="lineage.tsv"
String map_out="map_file.tsv"
}
command<<<

Expand All @@ -262,23 +265,25 @@ task stage {
fi
}

stage ~{contig_file} ~{contigs_out}
stage ~{sam_file} ~{bam_out}
stage ~{gff_file} ~{gff_out}
stage ~{proteins_file} ~{proteins_out}
stage ~{cog_file} ~{cog_out}
stage ~{ec_file} ~{ec_out}
stage ~{ko_file} ~{ko_out}
stage ~{pfam_file} ~{pfam_out}
stage ~{tigrfam_file} ~{tigrfam_out}
stage ~{cath_funfam_file} ~{cath_funfam_out}
stage ~{smart_file} ~{smart_out}
stage ~{supfam_file} ~{supfam_out}
stage ~{product_names_file} ~{products_out}
stage ~{gene_phylogeny_file} ~{gene_phylogeny_out}
stage ~{contig_file} ~{contigs_out} &
stage ~{sam_file} ~{bam_out} &
stage ~{gff_file} ~{gff_out} &
stage ~{proteins_file} ~{proteins_out} &
stage ~{cog_file} ~{cog_out} &
stage ~{ec_file} ~{ec_out} &
stage ~{ko_file} ~{ko_out} &
stage ~{pfam_file} ~{pfam_out} &
stage ~{tigrfam_file} ~{tigrfam_out} &
stage ~{cath_funfam_file} ~{cath_funfam_out} &
stage ~{smart_file} ~{smart_out} &
stage ~{supfam_file} ~{supfam_out} &
stage ~{product_names_file} ~{products_out} &
stage ~{gene_phylogeny_file} ~{gene_phylogeny_out} &
stage ~{lineage_file} ~{lineage_out}
~{"stage " + map_file + " " + map_out}
wait

date --iso-8601=seconds > start.txt
date --iso-8601=seconds > start.txt

>>>

Expand All @@ -298,6 +303,7 @@ task stage {
File product_names = "products.tsv"
File gene_phylogeny = "gene_phylogeny.tsv"
File lineage_tsv = "lineage.tsv"
File? map_tsv = map_out
String start = read_string("start.txt")
}
runtime {
Expand Down
2 changes: 1 addition & 1 deletion version.txt
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@@ -1 +1 @@
v1.3.5
v1.3.6
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