Minimal test file for conda error

test_minimal.snake

#/usr/bin/env python
import os

from lcdblib.snakemake import helpers
from lcdblib.utils import utils

URI = '../lcdb-wrapper-tests'
TMPDIR='/mnt/threeTB/centos_scratch'
references = {
    'dmel': {
        'gtf':  '/data/LCDB/lcdb-references/dmel/r6-11/gtf/dmel_r6-11.gtf',
        'hisat2': '/data/LCDB/lcdb-references/dmel/r6-11/hisat2/dmel_r6-11.1.ht2',
        'refflat': '/data/LCDB/lcdb-references/dmel/r6-11/gtf/dmel_r6-11.refflat',
        },
    }

shell.prefix("set -euo pipefail; export TMPDIR={};".format(TMPDIR))

# Set working dir
workdir: '.'

def wrapper_for(path):
    return 'file:' + os.path.join(URI, 'wrappers', path)

################################################################################
# Set up file naming patterns and targets
################################################################################
patterns = {
    'fastq_clean': {
        'r1': '../output/prealignment/raw/{experiment}/{sample}/{sample}_1.clean.fastq.gz',
        },
    'hisat2': {
        'bam': '../output/prealignment/raw/{experiment}/{sample}/{sample}.fq.bam',
        },
    'feature_counts': {
        'counts': '../output/prealignment/raw/{experiment}/{sample}/{sample}_{featurecount_strand}.fq.bam.counts',
        'summary': '../output/prealignment/raw/{experiment}/{sample}/{sample}_{featurecount_strand}.fq.bam.counts.summary',
    },
    'picard_collectrnaseqmetrics': {
        'metrics': '../output/prealignment/raw/{experiment}/{sample}/{sample}_{picard_collectrnaseqmetrics}.fq.bam.picard.metrics',
    },
}

# Build target files
targets = helpers.fill_patterns(patterns, {'sample': 'ERR489286', 'experiment': 'ERX455041', 'featurecount_strand': 1, 'picard_collectrnaseqmetrics': 'FIRST_READ_TRANSCRIPTION_STRAND'})
rule targets:
    input:
        utils.flatten(targets['feature_counts']) +
        utils.flatten(targets['picard_collectrnaseqmetrics'])

rule fastq_clean:
    output: r1=temp(patterns['fastq_clean']['r1'])
    conda: 'fastq_clean.yaml'
    shell:
        'fastq-dump -O $TMPDIR -X 1000000 --split-files --gzip {wildcards.sample} '
        '&& cp $TMPDIR/{wildcards.sample}_1.fastq.gz {output.r1} '
        '&& rm $TMPDIR/{wildcards.sample}_1.fastq.gz '

rule hisat2_fastq:
    input:
        index=references['dmel']['hisat2'],
        fastq=rules.fastq_clean.output.r1
    output: bam=temp(patterns['hisat2']['bam'])
    threads: 8
    log: patterns['hisat2']['bam'] + '.log'
    wrapper: wrapper_for('hisat2/align')

rule featurecounts:
    input:
        annotation=references['dmel']['gtf'],
        bam=patterns['hisat2']['bam']
    output:
        counts=patterns['feature_counts']['counts'],
        summary=patterns['feature_counts']['summary']
    params: extra='-s {featurecount_strand}'
    wrapper: wrapper_for('featurecounts')

rule collectrnaseqmetrics:
    input:
        bam=patterns['hisat2']['bam'],
        refflat=references['dmel']['refflat']
    output: metrics=patterns['picard_collectrnaseqmetrics']['metrics']
    params: extra='STRAND={picard_collectrnaseqmetrics}'
    log: patterns['picard_collectrnaseqmetrics']['metrics'] + '.log'
    wrapper: wrapper_for('picard/collectrnaseqmetrics')