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Build branch main with version main (bd5b2d4)

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Build pipeline: viash-hub.htrnaseq.main-l2658

Source commit: bd5b2d4171

Source message: Keep contents for barcodes with no mapped reads. (#44)
This commit is contained in:
CI
2025-02-21 11:49:43 +00:00
parent 6468e4a5de
commit e5a3fd36ee
71 changed files with 340 additions and 125 deletions
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2
target/executable/stats/combine_star_logs/.config.vsh.yaml
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@@ -198,7 +198,7 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.0"
git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/stats/combine_star_logs/combine_star_logs
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@@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
LABEL org.opencontainers.image.created="2025-02-21T11:03:28Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
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@@ -182,7 +182,7 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.0"
git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

26
target/executable/stats/generate_pool_statistics/generate_pool_statistics
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@@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z"
LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1044,6 +1044,7 @@ trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
import pandas as pd
from pathlib import Path
import re
### VIASH START
@@ -1085,20 +1086,25 @@ if __name__ == "__main__":
# nrReadsNrGenesPerChrom file
#########
nr_reads_nr_genes_wells = []
par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"]))
for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]:
nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file,
header=0, delimiter="\\t",
dtype={"WellBC": pd.StringDtype(),
"WellID": pd.StringDtype(),
"Chr": pd.StringDtype(),
"NumberOfReads": pd.UInt64Dtype(),
"NumberOfGenes": pd.UInt64Dtype()}))
nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file,
header=0, delimiter="\\t",
dtype={"WellBC": pd.StringDtype(),
"WellID": pd.StringDtype(),
"Chr": pd.StringDtype(),
"NumberOfReads": pd.UInt64Dtype(),
"NumberOfGenes": pd.UInt64Dtype()})
if nr_reads_nr_gene_well.empty:
raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!")
nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well)
nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,)
total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr",
values=["NumberOfReads"], fill_value=0,
aggfunc="sum").droplevel(0, axis=1)
total_nr_reads_per_chromosome.columns.name = None
# Remove scaffolds/chromosomes with no counts
total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)]
##### Total number of genes from all chromosomes
total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum()

2
target/executable/stats/generate_well_statistics/.config.vsh.yaml
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@@ -264,7 +264,7 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.0"
git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

5
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z"
LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b"
LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1259,6 +1259,7 @@ if __name__ == "__main__":
NumberOfReads=pd.NamedAgg("GX", aggfunc="size"),
NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique")
)
nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0)
logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s",
par['nrReadsNrGenesPerChrom'])
nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\\