Merge pull request #66 from gbouras13/pr-65

Pr 65

Author: gbouras13

.github/workflows/ci.yaml

@@ -57,5 +57,6 @@ jobs:
           just test-ci
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
-      
+        with:
+            use_node: true      
 

.github/workflows/release.yaml

@@ -39,4 +39,4 @@ jobs:
         uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
+          password: ${{ secrets.PYPI_TOKEN }}

README.md

@@ -222,7 +222,7 @@ You will then need to install the external dependencies separately, which can be
 * [Flye](https://github.com/fenderglass/Flye) >=2.9
 * [Unicycler](https://github.com/rrwick/Unicycler) >=0.4.8
 * [Minimap2](https://github.com/lh3/minimap2) >=2.11
-* [fastp](https://github.com/OpenGene/fastp) >=0.18.0
+* [fastp](https://github.com/OpenGene/fastp) >=0.24.2
 * [chopper](https://github.com/wdecoster/chopper) >=0.5.0
 * [mash](https://github.com/marbl/Mash) >=2.2
 * [Raven](https://github.com/lbcb-sci/raven) >=1.8

build/environment.yaml

@@ -7,7 +7,7 @@ dependencies:
   - flye >=2.9
   - unicycler >=0.4.8
   - minimap2 >=2.11
-  - fastp >=0.18.0
+  - fastp >=0.24.2
   - chopper >=0.5.0
   - mash >=2.2
   - raven-assembler >=1.8

docs/install.md

@@ -31,7 +31,7 @@ You will then need to install the external dependencies separately, which can be
 * [Flye](https://github.com/fenderglass/Flye) >=2.9
 * [Unicycler](https://github.com/rrwick/Unicycler) >=0.4.8
 * [Minimap2](https://github.com/lh3/minimap2) >=2.11
-* [fastp](https://github.com/OpenGene/fastp) >=0.18.0
+* [fastp](https://github.com/OpenGene/fastp) >=0.24.2
 * [chopper](https://github.com/wdecoster/chopper) >=0.5.0
 * [mash](https://github.com/marbl/Mash) >=2.2
 * [Raven](https://github.com/lbcb-sci/raven) >=1.8

src/plassembler/utils/VERSION

@@ -1 +1 @@
-1.7.0
+1.7.0

src/plassembler/utils/input_commands.py

@@ -293,7 +293,7 @@ def check_dependencies():
     # fastp
     try:
         process = sp.Popen(["fastp", "--version"], stdout=sp.PIPE, stderr=sp.PIPE)
-        _, fastp_out = process.communicate()
+        fastp_out, _ = process.communicate()
         fastp_version = fastp_out.decode()
         fastp_version = fastp_version.split("\n")[0].split(" ")[1]
         message = f"fastp v{fastp_version} found."