develop -> staging (#330) (#331)

* Integrate warp docsite with Algolia search (#324)

* Add algolia, also fix some minor issues.

* Update the colors.

* updated CEMBA RRID (#326)

* updated CEMBA RRID and docusaurus.config.js

* Fixed links to WARP docs (#327)

* non-optional input (#329)

Co-authored-by: Chengchen(Rex) Wang <14366016+rexwangcc@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Jessica Way <jway@broadinstitute.org>

Co-authored-by: Chengchen(Rex) Wang <14366016+rexwangcc@users.noreply.github.com>
Co-authored-by: ekiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: Jessica Way <jway@broadinstitute.org>

Author: 4 people

pipelines/broad/dna_seq/germline/single_sample/exome/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Exome Germline Single Sample documentation has moved! Read more about the [Exome Germline Single Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Exome_Germline_Single_Sample_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Exome Germline Single Sample documentation has moved! Read more about the [Exome Germline Single Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Exome Germline Single Sample summary
 

pipelines/broad/dna_seq/germline/single_sample/wgs/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Whole Genome Germline Single Sample documentation has moved! Read more about the [Whole Genome Germline Single Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Whole Genome Germline Single Sample documentation has moved! Read more about the [Whole Genome Germline Single Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Whole_Genome_Germline_Single_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Whole Genome Germline Single Sample summary
 

pipelines/broad/genotyping/illumina/IlluminaGenotypingArray.documentation.md

@@ -1,7 +1,7 @@
 
 ## Announcing a new site for WARP documentation!
 
-Illumina Genotyping Array documentation has moved! Read more about the [Illumina Genotyping Array Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Illumina_Genotyping_Arrays_Pipeline/IlluminaGenotypingArray.documentation.html) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Illumina Genotyping Array documentation has moved! Read more about the [Illumina Genotyping Array Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Illumina_Genotyping_Arrays_Pipeline/IlluminaGenotypingArray.documentation) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Illumina Genotyping Array summary
 

pipelines/cemba/cemba_methylcseq/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-CEMBA documentation has moved! Read more about the [CEMBA Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/CEMBA_MethylC_Seq_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+CEMBA documentation has moved! Read more about the [CEMBA Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### CEMBA summary
 

pipelines/skylab/optimus/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Optimus documentation has moved! Read more about the [Optimus Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Optimus_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Optimus documentation has moved! Read more about the [Optimus Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Optimus summary
 

pipelines/skylab/scATAC/README.md

@@ -1,7 +1,7 @@
 
 ## Announcing a new site for WARP documentation!
 
-scATAC documentation has moved! Read more about the [scATAC Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Single_Cell_ATAC_Seq_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+scATAC documentation has moved! Read more about the [scATAC Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### scATAC summary
 

pipelines/skylab/smartseq2_multisample/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Smart-seq2 Multi-Sample documentation has moved! Read more about the [Smart-seq2 Multi-Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Smart-seq2_Multi_Sample_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Smart-seq2 Multi-Sample documentation has moved! Read more about the [Smart-seq2 Multi-Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 
 ### Smart-seq2 Multi-Sample summary

pipelines/skylab/smartseq2_single_nucleus/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Smart-seq2 Single Nucleus documentation has moved! Read more about the [Smart-seq2 Single Nucleus Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Smart-seq2_Single_Nucleus_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Smart-seq2 Single Nucleus documentation has moved! Read more about the [Smart-seq2 Single Nucleus Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Nucleus_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Smart-seq2 Single Nucleus summary
 

pipelines/skylab/smartseq2_single_nucleus/SmartSeq2SingleNucleus.wdl

@@ -52,7 +52,7 @@ workflow SmartSeq2SingleNucleus {
   call TrimAdapters.TrimAdapters as TrimAdapters {
        input:
          fastq1 = fastq1,
-         fastq2 = select_first([fastq2]),
+         fastq2 = fastq2,
          adapter_list = adapter_list
    }
 

pipelines/skylab/smartseq2_single_nucleus_multisample/README.md

@@ -1,6 +1,6 @@
 ## Announcing a new site for WARP documentation!
 
-Smart-seq2 Single Nucleus Multi-Sample documentation has moved! Read more about the [Smart-seq2 Single Nucleus Multi-Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+Smart-seq2 Single Nucleus Multi-Sample documentation has moved! Read more about the [Smart-seq2 Single Nucleus Multi-Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!