Give assembly_improvement a pretty README

assembly_improvement/README.md

@@ -0,0 +1,37 @@
+# Assembly Improvement
+
+[![Container source](https://img.shields.io/static/v1?label=Container%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/MillironX/singularity-builds/tree/master/assembly_improvement)
+[![assembly_improvement source](https://img.shields.io/static/v1?label=assembly_improvement%20Source&message=GitHub&color=lightgrey&logo=github&style=flat-square)](https://github.com/sanger-pathogens/assembly_improvement)
+[![Version 1.160490](https://img.shields.io/static/v1?label=Latest%20version&message=1.160490&color=yellowgreen&logo=linuxcontainers&style=flat-square)](https://cloud.sylabs.io/library/millironx/default/assembly_improvement)
+[![Docs](https://img.shields.io/static/v1?label=Docs&message=README&color=blue&style=flat-square)](https://github.com/sanger-pathogens/assembly_improvement/blob/master/README.md)
+[![CentOS base](https://img.shields.io/static/v1?label=Base%20image&message=CentOS&color=9fcf32&logo=centos&style=flat-square)](https://www.centos.org/)
+
+Take in an assembly in FASTA format, reads in FASTQ format, and make the
+assembly better by scaffolding and gap filling.
+
+## Tools installed
+
+### SSPACE
+
+- `SSPACE_Basic.pl`
+
+### GapFiller
+
+- `GapFiller`
+
+### Abacas
+
+- `abacas.pl`
+
+### SGA
+
+- `sga`
+
+### improve_assembly
+
+- `improve_assembly`
+- `diginorm_with_khmer`
+- `fill_gaps_with_gapfiller`
+- `order_contigs_with_abacas`
+- `read_correction_with_sga`
+- `scaffold_with_sspace`

assembly_improvement/assembly_improvement.def

@@ -11,7 +11,7 @@ From: default/centos:latest
   dnf config-manager --set-enabled PowerTools
 
   # Operating dependencies
-  dnf --setopt=install_weak_deps=False install procps perl python3 -y
+  dnf --setopt=install_weak_deps=False install procps perl python3 which -y
 
   # Building dependencies
   dnf groupinstall 'Development Tools' -y
@@ -152,7 +152,7 @@ From: default/centos:latest
 %labels
   Author 25492070+MillironX@users.noreply.github.com
   SoftwareVersion 1.160490
-  SingularityDefinitionVersion 1
+  SingularityDefinitionVersion 2
 
 %help
   Assembly Improvement