clear error, fixes #962 (#966)

* clear error, fixes #962

* printf to convert \n to newline

---------

Co-authored-by: Siebren Frölich <48289046+siebrenf@users.noreply.github.com>

CHANGELOG.md

@@ -19,6 +19,7 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
 
 - edge case when a GSM sample is a reanalysis of another GSM sample.
 - error message referring to `--config` while it should be `--configfile`
+- clear error message when downloading single-end data annotated as paired-end.
 
 ## [0.9.8] - 2023-02-01
 

seq2science/rules/get_fastq.smk

@@ -150,10 +150,14 @@ rule sra2fastq_PE:
         --threads {threads} --split-e --skip-technical --dumpbase \
         --readids --clip --read-filter pass --defline-seq '@$ac.$si.$sg/$ri' \
         --defline-qual '+' --gzip >> {log} 2>&1
+        
+        # check if the files exist
+        if ! compgen -G "{output.tmpdir}/*_1*" > /dev/null ; then printf "ERROR: Couldn't find read 1.fastq after dumping! Perhaps this is not a paired-end file?\n" >> {log} 2>&1; fi
+        if ! compgen -G "{output.tmpdir}/*_2*" > /dev/null ; then printf "ERROR: Couldn't find read 2.fastq after dumping! Perhaps this is not a paired-end file?\n" >> {log} 2>&1; fi
 
         # rename file and move to output dir
-        mv {output.tmpdir}/*_1* {output.fastq[0]}
-        mv {output.tmpdir}/*_2* {output.fastq[1]}
+        mv {output.tmpdir}/*_1* {output.fastq[0]} >> {log} 2>&1
+        mv {output.tmpdir}/*_2* {output.fastq[1]} >> {log} 2>&1
         """