Mobile version| __ Datei 2
| __ Datei ... < /p>
Und schließlich würde die letzte Regel als Eingabemaßnahmen empfangen. ./Scoring_pipeline.sh ) und wird als Ausgabe einen Ordner mit dem Namen AccessIBioTHIAityOutput, einen Subordner mit Bildern und vielen TXT -Dateien angeben. | TranscriptionFactors
| GTRD_CHIP_ONLY_1000SITES
| < /strong> Datei 1
| Datei 2
| __ Datei ...
| AccessibilityOutput
| < /strong> {} Accessibility1KSITSAdjusted.txt
| < /em> _ {} Accessity1ksites.txt
| < /em> _ Datei ...
| Waveletout
| < /strong> Bild 1
| __ Bild 2
| __ Bild ...
| __ log.txt < /p>
Code: Select all
import os
configfile: "config.yaml"
SAMPLES = [d for d in os.listdir(config["input_folder"]) if os.path.isdir(os.path.join(config["input_folder"], d))]
#print(SAMPLES)
rule all:
input:
expand(config["output_folder"] + "/{sampleID}", sampleID=SAMPLES)
rule format_to_cn_seg_files:
input:
seg=config["seg_folder"] + "/{sampleID}.seg"
output:
filtered_seg="filtered_segs/{sampleID}_filtered.seg"
shell:
"""
mkdir -p filtered_segs
head -n 10 {input.seg} # Preview first 10 lines
awk '{{print $2 "\\t" $3 "\\t" $4 "\\t" $NF}}' {input.seg} > {output.filtered_seg}
awk '!($NF ~ /^NA$/)' {output.filtered_seg} > {output.filtered_seg}.tmp && mv {output.filtered_seg}.tmp {output.filtered_seg}
sed -i '1d' {output.filtered_seg}
sed -i '1i chr\\tstart\\tend\\tLog2-ratio' {output.filtered_seg}
"""
rule run_tf_analyses_from_bam:
input:
bam=config["input_folder"] + "/{sampleID}/{sampleID}.srtd.markdup.bam",
bai=config["input_folder"] + "/{sampleID}/{sampleID}.srtd.markdup.bam.bai",
seg="filtered_segs/{sampleID}_filtered.seg"
output:
directory(config["output_folder"] + "/{sampleID}")
shell:
"""
mkdir -p {output}
python {config[path_to_scripts]}/run_tf_analyses_from_bam_ori.py \\
-b {input.bam} \\
-o {output} \\
-norm-file {input.seg} -hg38 -a tf_gtrd_1000sites
"""
rule calculate_accessibility:
input:
tf_results=config["output_folder"] + "/{sampleID}" # Directorio con resultados anteriores
output:
directory(config["output_folder"] + "/{sampleID}")
message: "Executing calculate_accessibility with {input}."
shell:
"""
./scoring_pipeline.sh {input.tf_results} {wildcards.sampleID}
"""
< /code>
Das [url=viewtopic.php?t=11587]Problem[/url] ist, dass, wenn ich mit Snakemake einen Trocknungslauf trog versuche, nur Regel format_to_cn_seg_files und run_tf_analyses_from_bam
Dies ist die Ausgabe im Terminal: snakemake -s snakemake_all_process.smk -erkannt. n-Debug-dag Code: Select all
Building DAG of jobs...
candidate job all
wildcards:
candidate job calculate_accessibility
wildcards: sampleID=04B003764_R
candidate job run_tf_analyses_from_bam
wildcards: sampleID=04B003764_R
candidate job format_to_cn_seg_files
wildcards: sampleID=04B003764_R
selected job format_to_cn_seg_files
wildcards: sampleID=04B003764_R
selected job run_tf_analyses_from_bam
wildcards: sampleID=04B003764_R
candidate job calculate_accessibility
wildcards: sampleID=VH_14B_019722_R
candidate job run_tf_analyses_from_bam
wildcards: sampleID=VH_14B_019722_R
candidate job format_to_cn_seg_files
wildcards: sampleID=VH_14B_019722_R
selected job format_to_cn_seg_files
wildcards: sampleID=VH_14B_019722_R
selected job run_tf_analyses_from_bam
wildcards: sampleID=VH_14B_019722_R
selected job all
wildcards:
Job stats:
job count
------------------------ -------
all 1
format_to_cn_seg_files 2
run_tf_analyses_from_bam 2
total 5
Reasons:
(check individual jobs above for details)
input files updated by another job:
all, run_tf_analyses_from_bam
output files have to be generated:
run_tf_analyses_from_bam
set of input files has changed since last execution:
format_to_cn_seg_files
Some jobs were triggered by provenance information, see 'reason' section in the rule displays above.
If you prefer that only modification time is used to determine whether a job shall be executed, use the command line option '--rerun-triggers mtime' (also see --help).
If you are sure that a change for a certain output file (say, ) won't change the result (e.g. because you just changed the formatting of a script or environment definition), you can also wipe its metadata to skip such a trigger via 'snakemake --cleanup-metadata '.
Rules with provenance triggered jobs: format_to_cn_seg_files
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.