From ea979e85f57c610eb451e5a5fc0ee20710b2a7bb Mon Sep 17 00:00:00 2001 From: scaketti Date: Tue, 26 Aug 2025 15:03:06 -0300 Subject: [PATCH] =?UTF-8?q?Corrigindo=20problemas=20ao=20executar=20o=20wo?= =?UTF-8?q?rkflow=20em=20um=20servidor=20HPC.=20Ao=20testar,=20retornava?= =?UTF-8?q?=20um=20erro=20de=20conex=C3=A3o=20recusada=20do=20FTP,=20por?= =?UTF-8?q?=20conta=20da=20tentativa=20de=20download=20em=20paralelo.=20Al?= =?UTF-8?q?=C3=A9m=20disso,=20o=20nome=20de=20arquivo=20de=20exemplo=20par?= =?UTF-8?q?a=20a=20variavel=20"ref=5Fgenome"=20deixava=20o=20usu=C3=A1rio?= =?UTF-8?q?=20em=20d=C3=BAvida=20sobre=20qual=20tipo=20de=20dado=20=C3=A9?= =?UTF-8?q?=20utilizado=20como=20entrada.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Arquivos modificados: - config/nexflow.config: alterando o nome do arquivo esperado para "ref_genome" - modules/downloadReadFTP.nf: adicionando o parâmetro "maxForks", limitando o número de conexões simultâneas para download dos dados. --- config/nextflow.config | 2 +- modules/downloadReadFTP.nf | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/config/nextflow.config b/config/nextflow.config index 96a9109..a1cc4e1 100644 --- a/config/nextflow.config +++ b/config/nextflow.config @@ -5,7 +5,7 @@ params { report_dir = 'report' publish_dir_mode = 'symlink' // avoid duplicating output files (I think we should always try to use symlink instead of copy mode) samples_csv = "$projectDir/../samples/samples.csv" - ref_genome = "$projectDir/../references/cds_from_genomic.fna" + ref_genome = "$projectDir/../references/mrna_genomic_sequence.fna" // adicionar as sequencias genomicas dos mRNAs anotados } // OBS: that is just a draft version; we must try to remove every 'code smell' from our code (if possible) diff --git a/modules/downloadReadFTP.nf b/modules/downloadReadFTP.nf index 765d38c..ec92bab 100644 --- a/modules/downloadReadFTP.nf +++ b/modules/downloadReadFTP.nf @@ -1,4 +1,6 @@ process downloadReadFTP { + maxForks 2 // limit parallel downloads: https://github.com/nextflow-io/nextflow/discussions/3415 + input: tuple val(run), path(json_file)