WASHINGTON — Now that the Senate has passed its draft of the annual defense authorization bill, Capitol Hill staffers can begin the complicated process of trying to reconcile it with the House’s version in hopes of reaching compromise on a host of military policy issues.

But some of the most controversial topics are already off the table, due to Senate leadership’s decision to sideline a collection of controversial amendments. If a policy issue isn’t included in either chamber’s authorization legislation, lawmakers generally cannot include it in intramural conference.

In the conference, the House and Senate will have to hammer out their differences before a final version of the bill can be sent to the White House for a signature from the president.

The conference committee will have to work quickly if they hope to pass a final version of the legislation before the end of the calendar year.

Typically, the reconciliation work on the two competing bills begins in late summer, but the Senate vote was delayed by more than a month because of the ongoing health care fight and the cancer diagnosis of Senate Armed Services Committee Chairman John McCain, R-Ariz.

Here’s a look at what items were left out of that upcoming conference committee work and what fights still lie ahead:

** UNDER DISCUSSION — A pay raise for troops

Troops will get a pay raise next year thanks to the final defense authorization bill. The only question that remains for lawmakers is how much.

The Senate has backed a 2.1 percent pay boost for troops starting in January, while the House has approved a 2.4 percent one. The Senate’s version syncs with the White House’s planned raise for next year, while the House plan equals the expected rise in private sector wages.

The differences between the plans is about $85 less a year for junior enlisted personnel, $130 for senior enlisted and junior officers, and $240 for mid-career officers. But it’s also about $200 million in federal spending, money Pentagon officials have said would be better spent on other training and readiness.

Despite agreeing with the president’s plan this year, the Senate authorization bill calls for tighter restrictions on White House plans to limit military pay boosts in the future. House members have not yet weighed in on that proposal.

** OFF THE TABLE — Base closings

McCain and others had hoped to include a new base closings proposal in the Senate’s draft of the military budget bill, but fights over other amendments blocked his ability to offer the proposal.

The result is another authorization bill without any provisions for a Base Realignment and Closure commission, despite repeated pleas from Pentagon officials to cut the military’s footprint across the country.

The Defense Department’s own studies have hinted that the armed forces may have up to 20 percent more capacity than the force needs now, but Defense Secretary James Mattis has publicly questioned the validity of that work in recent months. Nevertheless, the White House insists a base closing round could save billions annually.

But the idea remains unpopular with many in Congress, especially after the 2005 round produced fewer savings than military experts predicted. Expect the issue to come up again in next year’s budget debates.

** UNDER DISCUSSION — More troops

In contrast to former President Barack Obama’s plans for a smaller military force, Republican leaders in the House, Senate and executive branch are intent on boosting military end strength in coming years.

Last year, lawmakers approved an increase of 16,000 soldiers over Obama’s objections. In upcoming negotiations, they’ll have to decide how much further they want to go.

President Donald Trump has called for a boost of about 4,000 sailors for the Navy and another 4,100 airmen for the Air Force. The Senate’s plan calls for those increases plus 5,000 more active-duty soldiers, 1,000 more Marines, and 1,000 more Army reservists and Guardsmen.

But a plan outlined in the House draft of the authorization is even more ambitious. It calls for Trump’s additions plus another 1,700 members to the Air Force Reserves and Air National Guard, 1,000 to the Naval Reserve, 10,000 active-duty soldiers, 4,000 Army guardsmen and 3,000 Army Reservists.

Conference committee members will have to balance those increases with costs. The House plan is expected to add as much as $1.1 billion in additional spending annually, further boosting the country’s defense spending total.

** OFF THE TABLE — Transgender troops

Like the base closing issue, several senators had hoped to broach the issue of new limits on transgender individuals serving in the ranks during debate on the chamber floor last week, but those plans were shelved by Senate leadership.

Back in June, House members tried to do the opposite, unsuccessfully attempting to add language to their authorization bill that would prohibit the military from paying for transgender medical services. The issue became moot when Trump issued an executive order blocking those services later in the summer.

The end result is neither draft of the budget legislation includes transgender policy language. A bipartisan group of senators has offered stand-alone legislation to force Trump to allow those individuals to serve, but it won’t be included in conference negotiations.

Meanwhile, McCain has promised close oversight on the issue in months to come.

** UNDER DISCUSSION — More ships and aircraft

Trump touted his proposed fiscal 2018 budget as the first step in a multi-year rebuild of the military, but lawmakers in both chambers see opportunities for even more new platforms.

Trump’s plan calls for a ramp up of the embattled F-35 Joint Strike Fighter program, adding 70 new aircraft. The House plan calls for 87. The Senate’s version authorizes purchase of 94 of them. The Senate plan also calls for more F/A-18 Super Hornets for the Navy and more Army helicopters than either of the other two proposals.

Both House and Senate lawmakers backed plans to add five more Navy ships to the procurement plan for next year to the president’s slate of eight planned builds, but with significant differences in where the money should be spent.

That leaves the authorization conference committee with a common goal of more equipment purchases but a long list of details to work out.

** OFF THE TABLE — A new military force authorization

Sen. Rand Paul, R-Kent., had hoped to attach to the budget bill a rule mandating lawmakers repeal the existing use-of-force authorizations passed early in President George W. Bush’s tenure and replace them with updated guidelines for the conflicts in Iraq and Syria. But that bid failed last week when 61 senators voted to table the idea.

The authorization of military force issue has been a frequent topic of debate in Congress since 2014, when Obama first ordered airstrikes against Islamic State group fighters in Iraq.

But those discussions have produced little action. House lawmakers briefly attached a similar provision to a separate appropriations measure earlier this summer before leadership stripped it out. Paul’s amendment was the first real debate on the issue before the full Senate in the last six years.

If the issue is resolved in the near future, it won’t be in the defense budget bill. The House included no language on the issue in their draft, leaving it out of the final negotiations.

** UNDER DISCUSSION — Space Corps

House officials included in their authorization draft a proposal for U.S. Space Command, a new sub-unified command within Strategic Command. The command would operate as an independent service from the Air Force, a stark departure from the current set-up.

Military officials have been cool to the idea, and Senate officials included language to block the move. They also added language in the bill requiring the commander of Air Force Space Command serve a term of at least 6 years for continuity and stability assurances, further entrenching the existing structure.

House lawmakers argued the move would “delayer complicated bureaucracy in the Pentagon” and better prepare the country for future threats from space. But convincing conference negotiators to go along with the massive overhaul appears to be a difficult proposition.

**OFF THE TABLE — A spending cap fix

The total price tag on both the House and Senate budget proposals is close to $700 billion, once overseas contingency funds are factored in. That’s about $30 billion more than Trump’s own proposal.

But more importantly, all three violate mandatory spending caps in place for fiscal 2018. Unless Congress can reach a broader deal to adjust those caps, lawmakers will be constrained to a military base budget ceiling of $549 billion.

Conference committee negotiations won’t be debating a solution to that problem in their work, but they will be watching outside talks on the issue closely to adjust their authorization bill to appropriate measures.

That will likely mean the final conference draft won’t be finished until December, when Congress’ next budget deadline looms.