resolving a docker issue and making vcf annotation inputs optional

Dockerfile

@@ -20,6 +20,8 @@ RUN apt-get update && \
  make \
  gcc \
  cmake \
+ libxml2-dev \
+ libxslt-dev \
  git && \
  apt-get clean && \
  rm -rf /var/lib/apt/lists/* && \
@@ -50,7 +52,7 @@ RUN cd $HOME && PIXI_ARCH=x86_64 curl -fsSL https://pixi.sh/install.sh | bash
 ENV PATH $PATH:$HOME/.pixi/bin
 
 # 4) make the src directory required for PyPI dependencies and install everything
-RUN cd $HOME && mkdir /src && pixi install
+RUN cd $HOME && pixi install
 
 # 5) modify the shell config so that each container launches within the pixi env
 RUN echo "export PATH=$PATH:$HOME/.pixi/envs/default/bin" >> $HOME/.bashrc

main.nf

@@ -71,18 +71,13 @@ workflow {
  // Checking for required files
  // ---------------------------------------------------------------------- //
 
- // make sure provided refseq is provided and exists
+ // make sure a reference sequence FASTA, the minimum pipeline dependency, is
+ // provided and exists
  assert params.refseq :
  "Please provide a reference FASTA file with the parameter `refseq`."
  assert file(params.refseq).isFile() :
  "Please double check that the reference FASTA file provided with the parameter `refseq` exists."
 
- // make sure required snpeff config is provided and exists
- assert params.snpEff_config :
- "Please provide a snpEff config file with the parameter `snpEff_config`."
- assert file(params.snpEff_config).isFile() :
- "Please double check that the snpEff config file provided with the parameter `snpEff_config` exists."
-
  // ---------------------------------------------------------------------- //
 
  // initialize input channels
@@ -97,8 +92,9 @@ workflow {
  Channel.fromPath( params.ref_gbk ) :
  Channel.empty()
 
- ch_snpeff_config = Channel
- .fromPath( params.snpEff_config )
+ ch_snpeff_config = Channel ?
+ .fromPath( params.snpEff_config ) :
+ Channel.empty()
 
  // decide whether to run the ont or the illumina workflow
  if ( params.platform == "ont" ) {
@@ -114,7 +110,9 @@ workflow {
 
  ILLUMINA (
  ch_primer_bed,
- ch_refseq
+ ch_refseq,
+ ch_ref_gbk,
+ ch_snpeff_config
  )
 
  } else {

pyproject.toml

@@ -48,3 +48,4 @@ rust = ">=1.77.2,<1.80"
 csvtk = ">=0.30.0,<0.31"
 snpsift = ">=5.2,<6"
 loguru = ">=0.7.2,<0.8"
+lxml = ">=5.2.2,<5.3"

workflows/illumina.nf

@@ -14,6 +14,8 @@ workflow ILLUMINA {
  take:
  ch_primer_bed
  ch_refseq
+ ch_ref_gbk
+ ch_snpeff_config
 
  main:
  assert params.platform == "illumina"
@@ -67,7 +69,7 @@ workflow ILLUMINA {
  VARIANTS (
  ALIGNMENT.out,
  ch_refseq,
- ch_refgbk,
+ ch_ref_gbk,
  ch_snpeff_config
  )