Snakemake Input File Missing

[markpearl]

Hi There,

I've followed all of the install instructions, and now I seem to be running into permission issues. My yaml files all seem to be working correctly now, and it's successfully create a pool.

But some of the rules at the beginning of the Snakemake file seem to be causing a permission issues when creating directories.

Provided is the error I'm getting:

I've attached my snakefile and yaml files for the batch-shipyard configuration. Some help would be really appreciated on this! I've followed the installation guide very carefully so I think it's something specific with Snakemake. What's odd is that it works no problem when installing snakemake and the dependencies in Conda.

Snakefile for the RNA-Seq analysis pipeline using test data from zebrafish

You should not need to edit this file unless you are changing the programs in the pipeline

configfile: "config_zebrafish.yaml"
SAMPLES = config['samples']

R1_suffix=config['input_file_R1_suffix']
R2_suffix=config['input_file_R2_suffix']
genome_fasta_file = config['genome_fasta_file']
genome_index_base = config['genome_index_base']
merged_transcripts_file=config['merged_transcripts_file']

rule trim_and_qc_all:
input:
html=expand("{sample}_R1.trimmed_paired_fastqc.html", sample=SAMPLES)

rule trim_reads:
input:
R1_reads="data/{sample}" + R1_suffix,
R2_reads="data/{sample}" + R2_suffix
output:
"1_trimmed_reads/{sample}_R1.trimmed_paired.fastq",
"1_trimmed_reads/{sample}_R1.trimmed_unpaired.fastq",
"1_trimmed_reads/{sample}_R2.trimmed_paired.fastq",
"1_trimmed_reads/{sample}_R2.trimmed_unpaired.fastq"
threads: config['threads']
params:
run_params=config['trimmomatic_params']
shell:
"echo -e "#!/usr/bin/env bash\ncd $FILESHARE;\n trimmomatic PE -threads {threads} {input.R1_reads} {input.R2_reads} {output}" > $FILESHARE/jobrun.sh ;\n $SHIPYARD/shipyard jobs add --configdir $FILESHARE/azurebatch --tail stderr.txt\n"