logic error and wget fixes

replikation · Oct 6, 2021 · 5524460 · 5524460
1 parent 90f5c2e
commit 5524460
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Showing 4 changed files with 7 additions and 5 deletions.
diff --git a/modules/get_fast5_test_data.nf b/modules/get_fast5_test_data.nf
@@ -5,7 +5,7 @@ process get_fast5 {
 	path("fast5") 
 	script:
 	"""
-    wget https://osf.io/vxd7f/download -O SARSCoV2.tar.gz
+    wget --no-check-certificate https://osf.io/vxd7f/download -O SARSCoV2.tar.gz
     tar xzf SARSCoV2.tar.gz 
 	"""
 }
diff --git a/modules/get_fasta_test_data.nf b/modules/get_fasta_test_data.nf
@@ -5,6 +5,6 @@ process get_fasta {
 	path("SARSCoV2.fasta") 
 	script:
 	"""
-    wget https://osf.io/87bc9/download -O SARSCoV2.fasta
+    wget --no-check-certificate https://osf.io/87bc9/download -O SARSCoV2.fasta
 	"""
 }
diff --git a/modules/get_fastq_test_data.nf b/modules/get_fastq_test_data.nf
@@ -4,6 +4,6 @@ process get_nanopore_fastq {
 	path("SARSCoV2.fastq.gz") 
 	script:
 	"""
-    wget https://osf.io/kf54a/download -O SARSCoV2.fastq.gz
+    wget --no-check-certificate https://osf.io/kf54a/download -O SARSCoV2.fastq.gz
 	"""
 }
diff --git a/workflows/process/download_database_kraken2.nf b/workflows/process/download_database_kraken2.nf
@@ -6,12 +6,14 @@ process download_database_kraken2 {
     output:
         path("kraken.tar.gz")
     script:
-    if (task.attempt = 1)
+    if (task.attempt.toInteger() == 1)
         """
+        echo ${task.attempt}
         wget --no-check-certificate https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz -O kraken.tar.gz
         """
-    if (task.attempt > 1)
+    else if (task.attempt.toInteger() > 1)
         """
+        echo ${task.attempt}
         wget --no-check-certificate https://osf.io/eprfq/download -O kraken.tar.gz
         """
     stub: