Try another approach to fix the problem

snakecnv/align.snk

@@ -14,7 +14,7 @@ from align_snakemake_utils import SnakemakeUtils
 
 # Get from config:
 samples = get_samples_align(config['sample_file_align'])
-reference = os.path.abspath(config['reference'])
+reference = config['reference']
 wdir = config['wdir']
 
 workdir: wdir

snakecnv/detection.snk

@@ -54,7 +54,7 @@ message("Starting")
 FILTERBED = get_filterbed(config)
 EXCLUDEBED = get_excluded(config)
 
-REFERENCE = os.path.abspath(config['reference'])
+REFERENCE = config['reference']
 WDIR = config['wdir']
 workdir: WDIR
 

snakecnv/popsim.snk

@@ -84,8 +84,7 @@ rule get_fasta_popsim:
     input:
         "reference_raw.fasta"
     output:
-        "reference.fasta",
-        os.path.join(WDIR, "reference.fasta")
+        "reference.fasta"
     run:
         from Bio import SeqIO
         with open(input[0], "rU") as handle, open(output[0], "w") as f:

snakecnv/tools/delly.snk

@@ -10,6 +10,7 @@ rule delly:
         "{batch}/delly/delly_{chrom}_{svtype}.bcf"
     params:
         template = EMPTY_TEMPLATE
+        refrence = os.path.abspath(REFERENCE)
     threads:
         get_threads("delly", 4)
     log:
@@ -18,6 +19,6 @@ rule delly:
     shell:
         "export  OMP_NUM_THREADS={threads} ; "
         "delly.py -b {input.bamlist} -c {wildcards.chrom}"
-        " -g {input.reference} -x {input.excluded} -t {wildcards.svtype}"
+        " -g {params.reference} -x {input.excluded} -t {wildcards.svtype}"
         " -o {output} -e {params.template}"
         " 1>{log.stdout} 2>{log.stderr}"