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Don't know if this the right place to post this, m...
# fetchngs
s
Don't know if this the right place to post this, maybe #CJRH30T6V?, its regarding a module in fetchngs, 
sratools/fasterqdump
. I tried to modify the 
$args
via the module.config to add the 
--outfile
to rename the reads (suffix with a user-generated sample name). See below:
Copy code
withName: SRATOOLS_FASTERQDUMP {
        publishDir = [
            path: { "${params.outdir}" },
            mode: params.publish_dir_mode,
            pattern: 'reads/*.fastq.gz'
        ]
        def rename = {String sample_name, String accession -> "--outfile ${sample_name}_${accession}"}

        ext.args = {
            [
                meta.id ? rename(meta.id, meta.insdc_accession) : ""
            ].join(" ")
        }
    }
This worked when I ran the pipeline from the CLI but it breaks when I try and create a 
nf-test
for the "adding sample name" suffix case. Based on the 
.command.log
it looks like fasterq-dump is putting the 
_1
and 
_2
for paired reads in front of the 
.nf-test
folder in the file-path.
Copy code
Error: fasterq-dump cannot create this file: '~/fetchdatairidanext/_1.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/reads/S4SRR13191702'

	Error: fasterq-dump cannot create this file: '~/fetchdatairidanext/_2.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/reads/S4SRR13191702'
spots read      : 91
reads read      : 182
Since I do not want to remove the 
nf-tests
I was thinking I would have to modify the module to customize the reads filenames. It doesn't seem like 
pigz
has any options to modify reads names. It could be simply a fasterq-dump issue. I will continue to try and find an answer there. (Posting the full error log in comment)
The rest of the error log
Copy code
=============================================================
An error occurred during processing.
If the problem persists, you may consider sending the following XML document
to '<mailto:sra-tools@ncbi.nlm.nih.gov|sra-tools@ncbi.nlm.nih.gov>' for assistance.
=============================================================

<Report>
 <Run>
  <Date>
   <Start value="Thu Nov 7 2024 6:45:37 PM"/>
   <End value="Thu Nov 7 2024 6:45:37 PM"/>
  </Date>
  <Home name="HOME" value="/"/>
  <Cwd>~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773</Cwd>
  <CommandLine argc="8">
   <Arg index="0" value="fasterq-dump"/>
   <Arg index="1" value="--outfile"/>
   <Arg index="2" value="S4SRR13191702"/>
   <Arg index="3" value="--threads"/>
   <Arg index="4" value="4"/>
   <Arg index="5" value="--outdir"/>
   <Arg index="6" value="reads"/>
   <Arg index="7" value="SRR13191702"/>
  </CommandLine>
  <Result rc="RC(rcFS,rcDirectory,rcCreating,rcPath,rcNotFound)"/>
  <User admin="false"/>
 </Run>
 <Configuration>
  <Files count="3">
   <File name="~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/user-settings.mkfg"/>
   <File name="/usr/local/bin/ncbi/certs.kfg"/>
   <File name="/usr/local/bin/ncbi/default.kfg"/>
  </Files>
  <refseq state="not found"/>
  <krypto state="pwfile: not found"/>
  <sra>
   <quality_type>raw_scores</quality_type>
  </sra>
  <Config>  
  <ConfigurationFiles>
~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/user-settings.mkfg
/usr/local/bin/ncbi/certs.kfg
/usr/local/bin/ncbi/default.kfg
    </ConfigurationFiles>
    <APPNAME>"fasterq-dump"</APPNAME>
    <APPPATH>"~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/"</APPPATH>
    <BUILD>"RELEASE"</BUILD>
    <HOME>"/"</HOME>
    <HOST></HOST>
    <LIBS>
      <GUID>"79a16c17-e92a-4863-b17d-23a5da9c5a7a"</GUID>
    </LIBS>
    <NCBI_HOME>"//.ncbi"</NCBI_HOME>
    <NCBI_SETTINGS>"~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773/user-settings.mkfg"</NCBI_SETTINGS>
    <OS>"linux"</OS>
    <PWD>"~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773"</PWD>
    <USER></USER>
    <VDB_CONFIG></VDB_CONFIG>
    <VDB_ROOT></VDB_ROOT>
    <config>
      <default>"true"</default>
    </config>
    <kfg>
      <arch>
        <bits>"64"</bits>
        <name>"1446d6e7c79d"</name>
      </arch>
      <dir>"~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/71/857f2a47ddf2f331513106c0e69773"</dir>
      <name>"user-settings.mkfg"</name>
    </kfg>
    <libs>
      <cloud>
        <report_instance_identity>"true"</report_instance_identity>
      </cloud>
    </libs>
    <repository>
      <remote>
        <main>
          <SDL.2>
            <resolver-cgi>"<https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve>"</resolver-cgi>
          </SDL.2>
        </main>
        <protected>
          <SDL.2>
            <resolver-cgi>"<https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve>"</resolver-cgi>
          </SDL.2>
        </protected>
      </remote>
      <user>
        <ad>
          <public>
            <apps>
              <file>
                <volumes>
                  <flat></flat>
                  <flatAd>"."</flatAd>
                </volumes>
              </file>
              <refseq>
                <volumes>
                  <refseqAd>"."</refseqAd>
                </volumes>
              </refseq>
              <sra>
                <volumes>
                  <sraAd>"."</sraAd>
                </volumes>
              </sra>
              <sraPileup>
                <volumes>
                  <ad>"."</ad>
                </volumes>
              </sraPileup>
              <sraRealign>
                <volumes>
                  <ad>"."</ad>
                </volumes>
              </sraRealign>
              <wgs>
                <volumes>
                  <wgsAd>"."</wgsAd>
                </volumes>
              </wgs>
            </apps>
            <root>"."</root>
          </public>
        </ad>
        <main>
          <public>
            <apps>
              <file>
                <volumes>
                  <flat>"files"</flat>
                </volumes>
              </file>
              <nakmer>
                <volumes>
                  <nakmerFlat>"nannot"</nakmerFlat>
                </volumes>
              </nakmer>
              <nannot>
                <volumes>
                  <nannotFlat>"nannot"</nannotFlat>
                </volumes>
              </nannot>
              <refseq>
                <volumes>
                  <refseq>"refseq"</refseq>
                </volumes>
              </refseq>
              <sra>
                <volumes>
                  <sraFlat>"sra"</sraFlat>
                </volumes>
              </sra>
              <sraPileup>
                <volumes>
                  <withExtFlat>"sra"</withExtFlat>
                </volumes>
              </sraPileup>
              <sraRealign>
                <volumes>
                  <withExtFlat>"sra"</withExtFlat>
                </volumes>
              </sraRealign>
              <wgs>
                <volumes>
                  <wgsFlat>"wgs"</wgsFlat>
                </volumes>
              </wgs>
            </apps>
          </public>
        </main>
      </user>
    </repository>
    <sra>
      <quality_type>"raw_scores"</quality_type>
    </sra>
    <strings>
      <sdl>"<https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve>"</sdl>
    </strings>
    <tls>
      <ca.crt>
        <ncbi1>"-----BEGIN CERTIFICATE-----\x0D\x0AMIIDrzCCApegAwIBAgIQCDvgVpBCRrGhdWrJWZHHSjANBgkqhkiG9w0BAQUFADBh\x0D\x0AMQswCQYDVQQGEwJVUzEVMBMGA1UEChMMRGlnaUNlcnQgSW5jMRkwFwYDVQQLExB3\x0D\x0Ad3cuZGlnaWNlcnQuY29tMSAwHgYDVQQDExdEaWdpQ2VydCBHbG9iYWwgUm9vdCBD\x0D\x0AQTAeFw0wNjExMTAwMDAwMDBaFw0zMTExMTAwMDAwMDBaMGExCzAJBgNVBAYTAlVT\x0D\x0AMRUwEwYDVQQKEwxEaWdpQ2VydCBJbmMxGTAXBgNVBAsTEHd3dy5kaWdpY2VydC5j\x0D\x0Ab20xIDAeBgNVBAMTF0RpZ2lDZXJ0IEdsb2JhbCBSb290IENBMIIBIjANBgkqhkiG\x0D\x0A9w0BAQEFAAOCAQ8AMIIBCgKCAQEA4jvhEXLeqKTTo1eqUKKPC3eQyaKl7hLOllsB\x0D\x0ACSDMAZOnTjC3U/dDxGkAV53ijSLdhwZAAIEJzs4bg7/fzTtxRuLWZscFs3YnFo97\x0D\x0Anh6Vfe63SKMI2tavegw5BmV/Sl0fvBf4q77uKNd0f3p4mVmFaG5cIzJLv07A6Fpt\x0D\x0A43C/dxC//AH2hdmoRBBYMql1GNXRor5H4idq9Joz+EkIYIvUX7Q6hL+hqkpMfT7P\x0D\x0AT19sdl6gSzeRntwi5m3OFBqOasv+zbMUZBfHWymeMr/y7vrTC0LUq7dBMtoM1O/4\x0D\x0AgdW7jVg/tRvoSSiicNoxBN33shbyTApOB6jtSj1etX+jkMOvJwIDAQABo2MwYTAO\x0D\x0ABgNVHQ8BAf8EBAMCAYYwDwYDVR0TAQH/BAUwAwEB/zAdBgNVHQ4EFgQUA95QNVbR\x0D\x0ATLtm8KPiGxvDl7I90VUwHwYDVR0jBBgwFoAUA95QNVbRTLtm8KPiGxvDl7I90VUw\x0D\x0ADQYJKoZIhvcNAQEFBQADggEBAMucN6pIExIK+t1EnE9SsPTfrgT1eXkIoyQY/Esr\x0D\x0AhMAtudXH/vTBH1jLuG2cenTnmCmrEbXjcKChzUyImZOMkXDiqw8cvpOp/2PV5Adg\x0D\x0A06O/nVsJ8dWO41P0jmP6P6fbtGbfYmbW0W5BjfIttep3Sp+dWOIrWcBAI+0tKIJF\x0D\x0APnlUkiaY4IBIqDfv8NZ5YBberOgOzW6sRBc4L0na4UU+Krk2U886UAb3LujEV0ls\x0D\x0AYSEY1QSteDwsOoBrp+uvFRTp2InBuThs4pFsiv9kuXclVzDAGySj4dzp30d8tbQk\x0D\x0ACAUw7C29C79Fv1C5qfPrmAESrciIxpg0X40KPMbp1ZWVbd4wOTAeBggrBgEFBQcD\x0D\x0ABAYIKwYBBQUHAwEGCCsGAQUFBwMDDBdEaWdpQ2VydCBHbG9iYWwgUm9vdCBDQQ==\x0D\x0A-----END CERTIFICATE-----\x0D\x0A"</ncbi1>
        <ncbi2>"-----BEGIN CERTIFICATE-----\x0D\x0AMIIDxTCCAq2gAwIBAgIQAqxcJmoLQJuPC3nyrkYldzANBgkqhkiG9w0BAQUFADBs\x0D\x0AMQswCQYDVQQGEwJVUzEVMBMGA1UEChMMRGlnaUNlcnQgSW5jMRkwFwYDVQQLExB3\x0D\x0Ad3cuZGlnaWNlcnQuY29tMSswKQYDVQQDEyJEaWdpQ2VydCBIaWdoIEFzc3VyYW5j\x0D\x0AZSBFViBSb290IENBMB4XDTA2MTExMDAwMDAwMFoXDTMxMTExMDAwMDAwMFowbDEL\x0D\x0AMAkGA1UEBhMCVVMxFTATBgNVBAoTDERpZ2lDZXJ0IEluYzEZMBcGA1UECxMQd3d3\x0D\x0ALmRpZ2ljZXJ0LmNvbTErMCkGA1UEAxMiRGlnaUNlcnQgSGlnaCBBc3N1cmFuY2Ug\x0D\x0ARVYgUm9vdCBDQTCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAMbM5XPm\x0D\x0A+9S75S0tMqbf5YE/yc0lSbZxKsPVlDRnogocsF9ppkCxxLeyj9CYpKlBWTrT3JTW\x0D\x0APNt0OKRKzE0lgvdKpVMSOO7zSW1xkX5jtqumX8OkhPhPYlG++MXs2ziS4wblCJEM\x0D\x0AxChBVfvLWokVfnHoNb9Ncgk9vjo4UFt3MRuNs8ckRZqnrG0AFFoEt7oT61EKmEFB\x0D\x0AIk5lYYeBQVCmeVyJ3hlKV9Uu5l0cUyx+mM0aBhakaHPQNAQTXKFx01p8VdteZOE3\x0D\x0AhzBWBOURtCmAEvF5OYiiAhF8J2a3iLd48soKqDirCmTCv2ZdlYTBoSUeh10aUAsg\x0D\x0AEsxBu24LUTi4S8sCAwEAAaNjMGEwDgYDVR0PAQH/BAQDAgGGMA8GA1UdEwEB/wQF\x0D\x0AMAMBAf8wHQYDVR0OBBYEFLE+w2kD+L9HAdSYJhoIAu9jZCvDMB8GA1UdIwQYMBaA\x0D\x0AFLE+w2kD+L9HAdSYJhoIAu9jZCvDMA0GCSqGSIb3DQEBBQUAA4IBAQAcGgaX3Nec\x0D\x0AnzyIZgYIVyHbIUf4KmeqvxgydkAQV8GK83rZEWWONfqe/EW1ntlMMUu4kehDLI6z\x0D\x0AeM7b41N5cdblIZQB2lWHmiRk9opmzN6cN82oNLFpmyPInngiK3BD41VHMWEZ71jF\x0D\x0AhS9OMPagMRYjyOfiZRYzy78aG6A9+MpeizGLYAiJLQwGXFK3xPkKmNEVX58Svnw2\x0D\x0AYzi9RKR/5CYrCsSXaQ3pjOLAEFe4yHYSkVXySGnYvCoCWw9E1CAx2/S6cCZdkGCe\x0D\x0AvEsXCS+0yx5DaMkHJ8HSXPfqIbloEpw8nL+e/IBcm2PN7EeqJSdnoDfzAIJ9VNep\x0D\x0A+OkuE6N36B9KMEQwHgYIKwYBBQUHAwQGCCsGAQUFBwMBBggrBgEFBQcDAwwiRGln\x0D\x0AaUNlcnQgSGlnaCBBc3N1cmFuY2UgRVYgUm9vdCBDQQ==\x0D\x0A-----END CERTIFICATE-----\x0D\x0A"</ncbi2>
      </ca.crt>
    </tls>
    <tools>
      <ascp>
        <max_rate>"450m"</max_rate>
      </ascp>
    </tools>
    <vdb>
      <lib>
        <paths>
          <kfg>"/usr/local/bin"</kfg>
        </paths>
      </lib>
      <schema>
        <version>"2"</version>
      </schema>
    </vdb>
  </Config>
  <RemoteAccess available="true"/>
  <CurrentProtectedRepository found="false"/>
 </Configuration>
 <Object path="~/fetchdatairidanext/.nf-test/tests/3c9ac3ad622ddf71cd62aa4bbd87974d/work/95/affa0523ea101fa425b7624d7422eb/SRR13191702/SRR13191702.sra" type="database" fs_type="archive" size="113139">
  <Dependencies>
   <List count="0" missing="0">
   </List>
  </Dependencies>
 </Object>
 <SOFTWARE>
  <VDBLibrary vers="3.0.8"/>
  <Build static="true">
   <Module name=""/>
  </Build>
  <Tool date="Sep 19 2023" name="fasterq-dump" vers="3.0.8">
   <Binary path="/usr/local/bin/fasterq-dump" type="alias" md5="0a8179a2868b5e0da60d82b8374b9289">
    <Alias resolved="sratools.3.0.8"/>
   </Binary>
  </Tool>
 </SOFTWARE>
 <Env>
 </Env>
</Report>

fasterq-dump quit with error code 3
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