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Merge pull request #1 from tbooth/tim_branch
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feat: Print an immediate error if no input samples were found.
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LiaOb21 authored Mar 7, 2024
2 parents 34c590f + e3bf6ac commit 94bc243
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Showing 2 changed files with 12 additions and 13 deletions.
17 changes: 5 additions & 12 deletions workflow/Snakefile
Original file line number Diff line number Diff line change
@@ -1,21 +1,14 @@
# Main entrypoint of the workflow.
# Please follow the best practices:
# Main Snakefile and entry point of the workflow.
# Please see the best practices:
# https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html,
# in particular regarding the standardized folder structure mentioned there.


# Main Snakefile


# set config file where you can specify your inputs
configfile: "config/config.yaml"


# import glob to read {sample}
import glob

# set {samples} wildcard
samples = glob_wildcards(config["hic_path"] + "{sample}_1.fastq.gz").sample
samples_in_pattern = "{sample}_1.fastq.gz"
samples = glob_wildcards(config["hic_path"] + samples_in_pattern).sample


# Include the hifi_prep rule
Expand Down Expand Up @@ -58,4 +51,4 @@ include: "rules/common.smk"
# input files are defined in the common.smk file
rule all:
input:
get_all_inputs(),
get_all_inputs
8 changes: 7 additions & 1 deletion workflow/rules/common.smk
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@@ -1,8 +1,14 @@
# Define function for the inputs to rule_all
# this rule just defines the inputs to the final rule

def get_all_inputs(wc=None):
if not samples:
# Show the user a meaningful error message
logger.error(f"No files matching {samples_in_pattern} were found in"
f" {config.get('hic_path')}. Please check your config file.")
logger.error(f"Exiting.")
sys.exit(1)

def get_all_inputs():
inputs = [
"results/reads/hifi/hifi.fastq.gz", # output of hifi_prep rule
"results/nanoplot/NanoPlot-report.html", # nanoplot report
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