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Document running Syntelogfinder on test data
Added instructions for running Syntelogfinder on test data, including setup commands and expected runtime.
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docs/source/syntelogfinder.rst

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@@ -89,6 +89,25 @@ The ``params.json`` should look like this::
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"outdir": "output_path"
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}
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Running Syntelogfinder on test data
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-----------------------------------
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After downloading the fasta and gtf file and preperation of the parameter file the pipeline can be run like this:
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.. code-block:: bash
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git clone https://github.com/NIB-SI/syntelogfinder.git --branch v1.0.0
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cd syntelogfinder
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conda create -n nextflow -c bioconda nextflow
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conda activate nextflow
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nextflow run main.nf \
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-params-file params/params_test.json \
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-profile singularity \
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--run_blast \
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-resume
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**Expected runtime:** 10 minutes (if all singularity images are already pulled)
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Tutorial
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--------
@@ -173,4 +192,4 @@ Troubleshooting
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----------------
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- If GENESPACE process is interrupted, running with ``-resume`` flag will fail. To cache the other processes, delete the genespace work dir before resuming
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- If GENESPACE process is interrupted, running with ``-resume`` flag will fail. To cache the other processes, delete the genespace work dir before resuming

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