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nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
https://nf-co.re/circdna
MIT License
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Bug in line 214 of the nextflow.config file #29

Closed daianna21 closed 2 years ago

daianna21 commented 2 years ago

Description of the bug

When trying to run you circdna pipeline I get this error:

$ nextflow run nf-core/circdna --input samplesheet.csv --outdir results2 --genome GRCh38 --circle_identifier circle_map_realign,unicycler

NOTE: Nextflow is not tested with Java 1.8.0_121 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.3
Pulling nf-core/circdna ...
Project config file is malformed -- Cause: Compile failed for sources FixedSetSources[name='/groovy/script/Script6453BF79C0729536D1DCD438CC9F093E/_nf_config_cbad999a']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/groovy/script/Script6453BF79C0729536D1DCD438CC9F093E/_nf_config_cbad999a: 214: Unexpected character: '\'' @ line 214, column 23.
       version         = '1.0.0
                         ^

1 error

It turns out that a " ' " is missing at the end of the line 214 of that file. version = '1.0.0

Command used and terminal output

$ nextflow run nf-core/circdna --input samplesheet.csv --outdir results2 --genome GRCh38 --circle_identifier circle_map_realign,unicycler

NOTE: Nextflow is not tested with Java 1.8.0_121 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.3
Pulling nf-core/circdna ...
Project config file is malformed -- Cause: Compile failed for sources FixedSetSources[name='/groovy/script/Script6453BF79C0729536D1DCD438CC9F093E/_nf_config_cbad999a']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/groovy/script/Script6453BF79C0729536D1DCD438CC9F093E/_nf_config_cbad999a: 214: Unexpected character: '\'' @ line 214, column 23.
       version         = '1.0.0
                         ^

1 error

Relevant files

No response

System information

Version: 22.04.3 build 5703 System: Linux 2.6.32-696.28.1.el6.x86_64 Runtime: Groovy 3.0.10 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b31 Encoding: UTF-8 (UTF-8) No container engine used

sguizard commented 2 years ago

There is a missing quote in version string. @DSchreyer is working on an update that will fix this issue.

DSchreyer commented 2 years ago

Yes, v1.0.1 will fix this issue.

DSchreyer commented 2 years ago

Thanks for bringing this up. The bug was fixed in version 1.0.1