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clear error, fixes #962 #966

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Mar 21, 2023
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clear error, fixes #962 #966

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280800f
clear error, fixes #962
Maarten-vd-Sande Mar 21, 2023
8fdeab3
printf to convert \n to newline
siebrenf Mar 21, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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8 changes: 6 additions & 2 deletions seq2science/rules/get_fastq.smk
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Expand Up @@ -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
Comment on lines +155 to +156
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I did not know that echo doesn't work 😅 ... I did just now realize that the newline isn't even necessary, as echo automatically makes a newline. Do we know if printf is standard in bash?

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This is incredibly unclear to me for any command, but this post suggests to me it is


# 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
"""


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