Merge pull request #71 from Pathogen-Genomics-Cymru/https

https
Pathogen-Genomics-Cymru · Jul 12, 2024 · c23ac32 · c23ac32
2 parents cf7f2a5 + 74d8559
commit c23ac32
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/docker/Dockerfile.preprocessing-0.9.8 b/docker/Dockerfile.preprocessing-0.9.8
@@ -103,7 +103,7 @@ RUN curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_vers
 && unzip fastANI-Linux64-v${fastani_version}.zip \
 && mv fastANI /usr/local/bin
 
-RUN sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
+RUN sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
 && mkdir -p /opt/edirect \
 && mv /root/edirect/* /opt/edirect
 

diff --git a/modules/preprocessingModules.nf b/modules/preprocessingModules.nf
@@ -567,7 +567,7 @@ process downloadContamGenomes {
 
     """
     wget -i ${contam_list} --spider -nv -a linktestlog.txt 2>&1
-    grep -o 'ftp://.*fna.gz' linktestlog.txt > confirmedurllist.txt
+    grep -o 'https://.*fna.gz' linktestlog.txt > confirmedurllist.txt
 
     mkdir contam_dir
     cd contam_dir

diff --git a/singularity/Singularity.preprocessing-0.9.8 b/singularity/Singularity.preprocessing-0.9.8
@@ -109,7 +109,7 @@ curl -fsSL https://github.com/ArthurVM/Afanc/archive/refs/tags/v${afanc_version}
 && unzip fastANI-Linux64-v${fastani_version}.zip \
 && mv fastANI /usr/local/bin
 
-sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
+sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" \
 && mkdir -p /opt/edirect \
 && mv /root/edirect/* /opt/edirect